TF-NA Interface Dataset

Unique TF-NA Interfaces

This dataset characterizes unique transcription factor interfaces with nucleic acids based on interface identity.

Table S1.C: Unique interface between protein and nucleic acid present in transcription factors dataset.

PDB ID Protein Source
Organism		 Protein Length Experimental
Method		 Resolution
(Å)		 Oligomeric
State		 Unique Chains Chain BSA
Protein DNA RNA Complex Protein Nucleic
Acid
I. DNA-binding Transcription Factors
1A02 AP-1 FRAGMENT FOS +
NUCLEAR FACTOR OF ACTIVATED T CELLS		 H. sapiens 301+56 X 2.7 Homodimer +
Monomer		 NFJ:AB FJ AB - 2314 1207 1107
1A02 AP-1 FRAGMENT FOS +
NUCLEAR FACTOR OF ACTIVATED T CELLS		 H. sapiens 301+56 X 2.7 Homodimer + Monomer NFJ:AB N AB - 1860 952 908
1A0A PHOSPHATE SYSTEM POSITIVE
REGULATORY PROTEIN PHO4		 S. cerevisiae 63 X 2.8 Homodimer AB:CD AB CD - 2740 1429 1310
1AM9 STEROL REGULATORY ELEMENT
BINDING PROTEIN 1A		 H. sapiens 82 X 2.3 Homodimer

ABCD:

EFGH

 AB FG - 2699 1400 1299
1AN2 TRANSCRIPTION FACTOR MAX
(TF MAX)		 H. sapiens 86 X 2.9 Homodimer A:B AC BD - 2566 1286 1280
1AN4 UPSTREAM STIMULATORY FACTOR H. sapiens 65 X 2.9 Homodimer AB:CD AB CD - 2839 1438 1401
1APL MAT-ALPHA2 HOMEODOMAIN S. cerevisiae 83 X 2.7 Monomer CD:AB CD AB - 3519 1856 1662
1AWC GA BINDING PROTEIN ALPHA +
GA BINDING PROTEIN BETA 1		 M. musculus 110+153 X 2.2 Heterodimer AB:DE AB DE - 1526 728 798
1B01 TRANSCRIPTIONAL REPRESSOR COPG S. agalactiae 45 X 2.6 Homodimer AB:EF AB EF - 1429 717 712
1B3T NUCLEAR PROTEIN EBNA1 E. virus 147 X 2.2 Homodimer AB:CD AB CD - 5243 2616 2627
1B72 HOMEOBOX PROTEIN HOX-B1 +
PBX1		 H. sapiens 87+97 X 2.4 Heterodimer AB:DE A DE - 1590 810 780
1B72 HOMEOBOX PROTEIN HOX-B1 +
PBX1		 H. sapiens 87+97 X 2.4 Heterodimer AB:DE B DE - 1759 915 844
1BC8 SAP-1 ETS DOMAIN H. sapiens 93 X 1.9 Monomer C:AB C AB - 1710 816 894
1BF5 SIGNAL TRANSDUCER AND ACTIVATOR
OF TRANSCRIPTION 1-ALPHA/BETA		 H. sapiens 575 X 2.9 Homodimer A:BC AB CD - 3011 1511 1500
1BL0 MULTIPLE ANTIBIOTIC RESISTANCE PROTEIN E. coli 129 X 2.3 Monomer A:BC A BC - 2407 1201 1206
1BVO TRANSCRIPTION FACTOR GAMBIF1 A. gambiae 175 X 2.7 Monomer A:DE AB CD - 741 407 334
1CF7 TRANSCRIPTION FACTOR DP-2 +
TRANSCRIPTION FACTOR E2F-4		 H. sapiens 76+95 X 2.6 Heterodimer AB:CD A CD - 1552 801 751
1CF7 TRANSCRIPTION FACTOR DP-2 +
TRANSCRIPTION FACTOR E2F-4		 H. sapiens 76+95 X 2.6 Heterodimer AB:CD B CD - 1193 629 565
1CGP CATABOLITE GENE ACTIVATOR
PROTEIN (CAP)		 E. coli 205 X 3.0 Homodimer AB:CDEF AB DE - 1487 748 739
1CGP CATABOLITE GENE ACTIVATOR
PROTEIN (CAP)		 E. coli 205 X 3.0 Homodimer AB:CDEF AB CF - 1598 807 790
1CKT HIGH MOBILITY GROUP 1 PROTEIN R. norvegicus 71 X 2.5 Monomer A:BC A BC - 1630 839 791
1CMA MET REPRESSOR E. coli 104 X 2.8 Homodimer AB:CD AB CD - 1738 839 899
1D66 GAL4 S. cerevisiae 66 X 2.7 Homo 2-mer AB:DE AB DE - 2445 1191 1254
1DDN DIPHTHERIA TOX REPRESSOR C. diphtheriae 226 X 3.0 Homo 4-mer ABCD:EF ABCD EF - 5678 2801 2877
1DH3 TRANSCRIPTION FACTOR CREB M. musculus 55 X 3.0 Homodimer AC:BD AC BD - 2350 1204 1145
1DP7 MHC CLASS II TRANSCRIPTION
FACTOR HRFX1		 H. sapiens 76 X 1.5 Homo 2-mer P:D P AD - 1751 923 828
1DP7 MHC CLASS II TRANSCRIPTION
FACTOR HRFX1		 H. sapiens 76 X 1.5 Homo 2-mer P:D B AD - 1751 923 828
1EFA LAC REPRESSOR E. coli 333 X 2.6 Homodimer ABC:DE AB DE - 3517 1740 1777
1EGW MADS BOX TRANSCRIPTION ENHANCER FACTOR 2,
POLYPEPTIDE A		 H. sapiens 77 X 1.5 Homodimer

ABCD:

EFGH

 AB EF - 2910 1568 1343
1EXJ MULTIDRUG-EFFLUX TRANSPORTER REGULATOR B. subtilis 278 X 3.0 Homodimer A:M AB CM - 2263 1067 1196
1GD2 TRANSCRIPTION FACTOR PAP1 S. pombe 70 X 2.0 Homodimer

EFGHIJ:

ABCD

 EF AB - 2660 1401 1259
1GLU GLUCOCORTICOID RECEPTOR R. norvegicus 81 X 2.9 Homodimer AB:CD AB CD - 2634 1256 1378
1GT0 OCTAMER-BINDING TRANSCRIPTION FACTOR 1 +
TRANSCRIPTION FACTOR SOX-2		 M. musculus 159+80 X 2.6 Hetero 2-mer CD:AB CD AB - 5483 2839 2644
1GXP PHOSPHATE REGULON TRANSCRIPTIONAL
REGULATORY PROTEIN		 E. coli 106 X 2.5 Homodimer

ABEF:

CDGH

 AB CD - 3435 1715 1720
1H88 CCAAT/ENHANCER BINDING PROTEIN BETA +
MYB PROTO-ONCOGENE PROTEIN		 M. musculus 159+78 X 2.8 Homodimer + Monomer ABC:DE AB DE - 2499 1311 1188
1H88 CCAAT/ENHANCER BINDING PROTEIN BETA +
MYB PROTO-ONCOGENE PROTEIN		 M. musculus 159+78 X 2.8 Homodimer + Monomer ABC:DE C DE - 1997 1032 965
1HDD ENGRAILED HOMEODOMAIN D. melanogaster 61 X 2.8 Homo 2-mer CD:AB C AB - 1771 918 853
1HDD ENGRAILED HOMEODOMAIN D. melanogaster 61 X 2.8 Homo 2-mer CD:AB D AB - 928 439 488
1HJB CCAAT/ENHANCER BINDING PROTEIN BETA +
RUNT-RELATED TRANSCRIPTION FACTOR 1		 M. musculus 123+87 X 3.0 Homodimer + Monomer

ABCDEF

:GHIJ

 AB GH - 2355 1214 1142
1HJB CCAAT/ENHANCER BINDING PROTEIN BETA +
RUNT-RELATED TRANSCRIPTION FACTOR 1		 M. musculus 123+87 X 3.0 Homodimer + Monomer

ABCDEF:

GHIJ

 C GH - 1430 760 669
1HWT HEME ACTIVATOR PROTEIN S. cerevisiae 81 X 2.5 Homodimer

CDGH:

ABEF

 CD AB - 2584 1349 1235
1IC8 HEPATOCYTE NUCLEAR FACTOR 1-ALPHA H. sapiens 194 X 2.6 Homodimer AB:EF AB EF - 4929 2494 2434
1IF1 INTERFERON REGULATORY FACTOR 1 M. musculus 113 X 3.0 Homo 2-mer AB:CD A C - 1924 907 1017
1IF1 INTERFERON REGULATORY FACTOR 1 M. musculus 113 X 3.0 Homo 2-mer AB:CD B D - 1967 937 1031
1IGN RAP1 S. cerevisiae 246 X 2.3 Monomer

AB:

CDEF

 A C - 2509 1207 1302
1IHF INTEGRATION HOST FACTOR ALPHA +
INTEGRATION HOST FACTOR BET) (IHF)		 E. coli 94+99 X 2.5 Hetero 2-mer

AB:

CDE

 AB CDE - 4755 2386 2369
1IO4 CAAT/ENHANCER BINDING PROTEIN BETA +
CORE-BINDING FACTOR, BETA SUBUNIT +
RUNT-RELATED TRANSCRIPTION FACTOR 1		 M. musculus 123+141+78 X 3.0 Hetero 4-mer

ABCD:

EF

 ABC EF - 3842 2046 1797
1JE8 Nitrate/Nitrite Response
Regulator Protein NARL		 E. coli 82 X 2.1 Homodimer

ABEF:

CDGH

 AB CD - 2946 1398 1547
1JFI TATA-BOX-BINDING PROTEIN (TBP) +
Transcription Regulator NC2 alpha chain +
Transcription Regulator NC2 beta chain		 H. sapiens 179+185+98 X 2.6 Hetero 3-mer ABC:DE ABC DE - 4253 2117 2136
1JMC REPLICATION PROTEIN A (RPA) H. sapiens 246 X 2.4 Monomer A:B A B - 2184 1023 1161
1JT0 HYPOTHETICAL TRANSCRIPTIONAL
REGULATOR IN QACA 5'REGION		 S. aureus 194 X 2.9 Homo 4-mer

ABCD:

EF

 AC EF - 2417 1193 1224
1KU7 sigma factor sigA T. aquaticus 73 X 2.4 Homodimer AD:BC AD BC - 1196 621 575
1L3L Transcriptional activator protein traR A. tumefaciens 234 X 1.7 Homodimer

ABCD:

EFGH

 BD EG - 2404 1182 1222
1LMB LAMBDA REPRESSOR E. phage lambda 92 X 1.8 Hetero 2-mer 12:34 34 12 - 2904 1450 1454
1LQ1 Stage 0 sporulation protein A B. subtilis 120 X 2.3 Homo 2-mer CD:EF CD EF - 2382 1171 1212
1MDY MYOD BHLH DOMAIN +
MYOD BHLH DOMAIN		 M. musculus 62+68 X 2.8 Homo 2-mer

ABCD:

EFGH

 AB EF - 2666 1389 1277
1MHD SMAD3 H. sapiens 132 X 2.8 Homo 2-mer AB:CD AB CD - 1857 962 895
1MNM MAT ALPHA-2 TRANSCRIPTIONAL REPRESSOR +
MCM1 TRANSCRIPTIONAL REGULATOR		 S. cerevisiae 100+87 X 2.3 Hetero 4-mer ABCD:EF AB EF - 3320 1627 1693
1MNN NDT80 protein S. cerevisiae 340 X 1.4 Monomer A:BC A BC - 2661 1369 1292
1N6J Calcineurin-binding protein Cabin 1 +
Myocyte-specific enhancer factor 2B		 H. sapiens 35+93 X 2.2 Hetero 3-mer ABG:CD AB CD - 2721 1410 1311
1NGM Transcription factor IIIB BRF1 subunit +
Transcription initiation factor TFIID		 S. cerevisiae 180+72 X 3.0 Hetero 2-mer

ABEFIJ

MN:

CDGHK

LOP

 AB CD - 3121 1535 1586
1NKP Max protein +
Myc proto-oncogene protein		 H. sapiens 83+88 X 1.8 Hetero 2-mer

ABDE:

FGHJ

 AB FG - 2794 1434 1360
1NLW MAD + MAX PROTEIN H. sapiens 76+80 X 2.0 Hetero 2-mer

ABDE:

FGHJ

 AB FG - 2679 1377 1302
1NVP TATA box binding protein +
Transcription initiation factor IIA alpha chain +
Transcription initiation factor IIA beta chain +
Transcription initiation factor IIA gamma chain		 H. sapiens

108+181

+57+76

 X 2.1 Hetero 4-mer ABCD:EF ACD EF - 3323 1654 1668
1OCT POU DOMAIN H. sapiens 156 X 3.0 Monomer C:AB C AB - 3157 1597 1560
1ODH MGCM1 M. musculus 174 X 2.9 Monomer A:CD A CD - 1808 921 886
1P51 DNA-binding protein HU N. sp. 94 X 2.5 Homodimer ABCD:EFIH ABCD EFIH - 7231 3665 3566
1PAR ARC REPRESSOR S. phage P22 53 X 2.6 Homo 4-mer ABCD:EF AB EF - 2010 976 1034
1PAR ARC REPRESSOR S. phage P22 53 X 2.6 Homo 4-mer ABCD:EF CD EF - 2134 1033 1102
1PDN PRD PAIRED D. melanogaster 128 X 2.5 Monomer C:AB C AB - 2562 1299 1263
1PNR PURINE REPRESSOR E. coli 340 X 2.7 Homodimer A:B AC BD - 3596 1813 1782
1PP7 39 kDa initiator binding protein T. vaginalis 131 X 2.5 Monomer U:EF U EF - 1989 1017 971
1PUE TRANSCRIPTION FACTOR
PU.1 (TF PU.1)		 M. musculus 89 X 2.1 Monomer EF:ABCD E AB - 2018 962 1056
1QPI TETRACYCLINE REPRESSOR E. coli 203 X 2.5 Homodimer A:MN AB CM - 1135 576 559
1QRV HIGH MOBILITY GROUP PROTEIN D D. melanogaster 73 X 2.2 Homo 2-mer AB:CD AB CD - 2505 1301 1204
1R71 Transcriptional repressor protein korB E. coli 178 X 2.2 Homo 2-mer

ABCD:

EIFJGLHK

 AB EF - 3390 1673 1717
1R8D transcription activator MtaN B. subtilis 109 X 2.7 Homodimer AB:CD AB CD - 3175 1535 1639
1RAM TRANSCRIPTION FACTOR NF-KB P65 M. musculus 273 X 2.7 Homo 2-mer AB:CD AB CD - 2982 1458 1524
1RZR Glucose-resistance amylase regulator +
Phosphocarrier protein HPr		 P. megaterium 332+88 X 2.8 Hetero 4-mer

GCADTYS:

HREB

 CG HR - 3399 1679 1721
1SAX Methicillin resistance regulatory
protein mecI		 S. aureus 123 X 2.8 Homodimer AB:CD AB CD - 3065 1541 1524
1SKN DNA-BINDING DOMAIN OF SKN-1 C. elegans 92 X 2.5 Monomer P:AB P AB - 1691 866 825
1SVC NUCLEAR FACTOR KAPPA-B (NF-KB) H. sapiens 365 X 2.6 Homodimer P:D PB AD - 4062 2065 1997
1T2K Cyclic-AMP-dependent transcription factor ATF-2 +
Interferon regulatory factor 3 +
Transcription factor AP-1		 H. sapiens 112+61+62 X 3.0 Hetero 4-mer ABCD:EF ABCD EF - 6018 2966 3052
1TQE Histone deacetylase 9 +
Myocyte-specific enhancer factor 2B		 M. musculus 26+93 X 2.7 Hetero 3-mer

PQXRSY:

CDEF

 PQ CD - 3137 1630 1507
1TRR TRP REPRESSOR E. coli 107 X 2.4 Homo 4-mer

ABDE

GHJK:

CFIL

 AB CI - 2937 1446 1491
1TTU lin-12 And Glp-1 transcriptional regulator C. elegans 477 X 2.9 Monomer A:BC A BC - 2138 1082 1055
1TUP P53 TUMOR SUPPRESSOR H. sapiens 219 X 2.2 Homo 3-mer ABC:EF B EF - 1179 620 558
1TUP P53 TUMOR SUPPRESSOR H. sapiens 219 X 2.2 Homo 3-mer ABC:EF C EF - 630 309 321
1U8B Ada polyprotein E. coli 133 X 2.1 Monomer A:BCDE A BCDE - 2173 1030 1143
1UUT REP PROTEIN A. virus 5 197 X 2.0 Monomer AB:CD AB CD - 1456 609 847
1VOL TATA BINDING PROTEIN (TBP) +
TRANSCRIPTION FACTOR IIB (TFIIB)		 A. thaliana 200+204 X 2.7 Hetero 2-mer AB:CD A CD - 1148 538 611
1VOL TATA BINDING PROTEIN (TBP) +
TRANSCRIPTION FACTOR IIB (TFIIB)		 A. thaliana 200+204 X 2.7 Hetero 2-mer AB:CD B CD - 2817 1401 1416
1VTN HNF-3/FORK HEAD DNA-RECOGNITION MOTIF H. sapiens 102 X 2.5 Monomer C:AB C AB - 2088 1055 1033
1W0T TELOMERIC REPEAT BINDING FACTOR 1 H. sapiens 53 X 2.0 Homo 2-mer AB:CD A CD - 1563 794 769
1W0T TELOMERIC REPEAT BINDING FACTOR 1 H. sapiens 53 X 2.0 Homo 2-mer AB:CD B CD - 1557 782 775
1XBR T PROTEIN X. laevis 184 X 2.5 Homodimer AB:CD AB CD - 4169 2112 2057
1XPX Protein prospero D. melanogaster 163 X 2.8 Monomer A:DC A DC - 847 446 401
1YRN MAT A1 HOMEODOMAIN +
MAT ALPHA2 HOMEODOMAIN		 S. cerevisiae 61+83 X 2.5 Hetero 2-mer AB:CD A CD - 1367 717 650
1YRN MAT A1 HOMEODOMAIN +
MAT ALPHA2 HOMEODOMAIN		 S. cerevisiae 61+83 X 2.5 Hetero 2-mer AB:CD B CD - 1994 1061 932
1YSA GCN4 S. cerevisiae 58 X 2.9 Homo 2-mer CD:AB CD AB - 2258 1172 1086
1YTB TATA BINDING PROTEIN (TBP) S. cerevisiae 180 X 1.8 Monomer AB:CD A C - 2985 1486 1499
1YTB TATA BINDING PROTEIN (TBP) S. cerevisiae 180 X 1.8 Monomer AB:CD B D - 2886 1438 1448
1YTF TATA BINDING PROTEIN (TBP) TRANSCRIPTION FACTOR IIA - TOA1C SUBUNIT +
TRANSCRIPTION FACTOR IIA - TOA1N SUBUNIT +
TRANSCRIPTION FACTOR IIA - TOA2 SUBUNIT		 S. cerevisiae

121+180

+53+79

 X 2.5 Hetero 4-mer ABCD:EF A EF - 2932 1467 1465
1YTF TATA BINDING PROTEIN (TBP) TRANSCRIPTION FACTOR IIA - TOA1C SUBUNIT +
TRANSCRIPTION FACTOR IIA - TOA1N SUBUNIT +
TRANSCRIPTION FACTOR IIA - TOA2 SUBUNIT		 S. cerevisiae

121+180

+53+79

 X 2.5 Hetero 4-mer ABCD:EF C EF - 409 210 199
1Z9C ZIF268 B. subtilis 87 X 2.6 Homo 2-mer

ABCDEF:

GHIJKL

 AB GH - 4126 2019 2107
1ZAA PROLINE UTILIZATION TRANSCRIPTION ACTIVATOR M. musculus 70 X 2.1 Monomer C:AB C AB - 2599 1393 1206
1ZME PROLINE UTILIZATION TRANSCRIPTION ACTIVATOR S. cerevisiae 70 X 2.5 Homodimer CD:AB CD AB - 2636 1310 1326
2A07 Forkhead box protein P2 H. sapiens 93 X 1.9 Homo 6-mer

FGHIJK:

ABCD

 FG AB - 998 479 519
2A07 Forkhead box protein P2 H. sapiens 93 X 1.9 Homo 6-mer

FGHIJK:

ABCD

 J AB - 1436 709 728
2A07 Forkhead box protein P2 H. sapiens 93 X 1.9 Homo 6-mer

FGHIJK:

ABCD

 J CD - 509 249 260
2BNW ORF OMEGA S. pyogenes 53 X 2.5 Homodimer

ABCD:

EFGH

 AB EF - 1429 696 733
2BNW ORF OMEGA S. pyogenes 53 X 2.5 Homodimer

ABCD:

EFGH

 CD EF - 1484 728 756
2BOP PROTEIN E2 B. papillomavirus type 1 85 X 1.7 Homodimer A:B A B - 692 355 336
2BSQ TRAFFICKING PROTEIN A +
TRAFFICKING PROTEIN B		 N. gonorrhoeae 146+77 X 3.0 Hetero 8-mer

ABCD

EFGH:

IJ

 EH IJ - 1471 747 724
2BSQ TRAFFICKING PROTEIN A +
TRAFFICKING PROTEIN B		 N. gonorrhoeae 146+77 X 3.0 Hetero 8-mer

ABCD

EFGH:

IJ

 FG IJ - 1455 721 734
2C62 ACTIVATED RNA POLYMERASE II
TRANSCRIPTIONAL COACTIVATOR P15		 H. sapiens 66 X 1.7 Homo 2-mer AB:C AB C - 3029 1458 1571
2C9L BZLF1 TRANS-ACTIVATOR PROTEIN E. virus 63 X 2.3 Homo 2-mer YZ:AB YZ AB - 2337 1181 1156
2D5V Hepatocyte nuclear factor 6 R. norvegicus 164 X 2.0 Monomer

AB:

CDEF

 AB CDEF - 5595 2826 2769
2E1C Putative HTH-type transcriptional
regulator PH1519		 P. horikoshii 171 X 2.1 Homodimer A:BD A BD - 1030 523 507
2ER8 Regulatory protein LEU3 S. cerevisiae 72 X 2.9 Homodimer

ABCD:

EFGH

 AB EF - 2794 1384 1410
2ES2 Cold shock protein cspB B. subtilis 67 X 1.8 Monomer A:B A B - 903 432 471
2GLI FIVE-FINGER GLI H. sapiens 155 X 2.6 Monomer A:CD A CD - 3121 1585 1537
2H27 RNA polymerase Sigma E factor E. coli 73 X 2.3 Monomer

AD:

BCEF

 AD BCEF - 2881 1487 1394
2NLL RETINOIC ACID RECEPTOR +
THYROID HORMONE RECEPTOR		 H. sapiens 103+66 X 1.9 Hetero 2-mer AB:CD A CD - 1188 591 597
2NLL RETINOIC ACID RECEPTOR +
THYROID HORMONE RECEPTOR		 H. sapiens 103+66 X 1.9 Hetero 2-mer AB:CD B CD - 2037 995 1042
2O49 DNA-binding protein SATB1 H. sapiens 93 X 2.0 Monomer A:BC A BC - 1108 557 552
2OR1 434 REPRESSOR E. phage 434 69 X 2.5 Homo 2-mer LR:AB L AB - 1492 758 733
2OR1 434 REPRESSOR E. phage 434 69 X 2.5 Homo 2-mer LR:AB R AB - 1394 691 703
2P5L Arginine repressor B. subtilis 64 X 2.9 Homodimer

CDGH:

ABEF

 CD AB - 2614 1296 1318
2QL2 Neurogenic differentiation factor 1 M. musculus 60 X 2.5 Homo 2-mer

ABCD:

EFGH

 AB EF - 2165 1102 1063
2R1J Repressor protein C2 S. phage P22 68 X 1.5 Homo 2-mer LR:BA L BA - 1325 628 697
2R1J Repressor protein C2 S. phage P22 68 X 1.5 Homo 2-mer LR:BA R BA - 1341 634 707
2RBF Bifunctional protein putA E. coli 54 X 2.3 Homodimer AB:CD AB CD - 1598 806 792
2UZK FORKHEAD BOX PROTEIN O3A H. sapiens 97 X 2.7 Monomer AC:BDEF AC BDEF - 3380 1679 1700
2VY1 PROTEIN LEAFY A. thaliana 194 X 2.1 Homodimer A:W A W - 860 432 429
2W7N TRFB TRANSCRIPTIONAL REPRESSOR PROTEIN E. coli 101 X 1.9 Homodimer AB:EFGH AB EFGH - 2999 1549 1450
2YPA LIM DOMAIN-BINDING PROTEIN 1 +
RHOMBOTIN-2 +
T-CELL ACUTE LYMPHOCYTIC LEUKEMIA PROTEIN 1 +
TRANSCRIPTION FACTOR E2-ALPHA		 H. sapiens

145+51

+82+91

 X 2.8 Hetero 4-mer ABCD:EF ABCD EF - 2239 1136 1103
2YVH Transcriptional regulator C. glutamicum 177 X 2.5 Homodimer

ABCD:

EFGH

 ABCD EFGH - 4985 2536 2449
2ZHG Redox-sensitive transcriptional
activator soxR		 E. coli 154 X 2.8 Homodimer A:B A B - 583 268 315
3A5T Transcription factor MafG M. musculus 107 X 2.8 Homodimer AB:CD AB CD - 2596 1343 1253
3BRD Lin-12 and glp-1 phenotype protein 1,
isoform a +
Protein lin-12		 C. elegans 29+477 X 2.2 Hetero 2-mer AD:BC AD BC - 2024 1040 984
3BS1 Accessory gene regulator protein A S. aureus 103 X 1.6 Monomer A:BC A BC - 1547 779 768
3CLC Regulatory protein E. sp. RFL1396 82 X 2.8 Homodimer ABCD:EF AB EF - 2647 1329 1318
3CLC Regulatory protein E. sp. RFL1396 82 X 2.8 Homodimer ABCD:EF CD EF - 2652 1330 1322
3D2W TAR DNA-binding protein 43 M. musculus 89 X 1.7 Homodimer A:B A BD - 1321 646 676
3D2W TAR DNA-binding protein 43 M. musculus 89 X 1.7 Homodimer A:B C BD - 1321 646 676
3DFX Trans-acting T-cell-specific
transcription factor GATA-3		 M. musculus 63 X 2.7 Homo 4-mer AB:XY AB XY - 3545 1792 1753
3DNV HTH-type transcriptional
regulator hipB +
Protein hipA		 E. coli 440+88 X 2.7 Homodimer AB:T B TE - 1237 615 622
3DNV HTH-type transcriptional
regulator hipB +
Protein hipA		 E. coli 440+88 X 2.7 Homodimer AB:T D TE - 1237 615 622
3E6C Cyclic nucleotide-binding protein D. hafniense 250 X 1.8 Homodimer C:BA CF ABDE - 1353 653 700
3EYI Z-DNA-binding protein 1 H. sapiens 72 X 1.5 Homo 2-mer AB:CD A CD - 841 420 421
3EYI Z-DNA-binding protein 1 H. sapiens 72 X 1.5 Homo 2-mer AB:CD B CD - 622 300 322
3FDQ Motility gene repressor mogR L. monocytogenes serovar 1/2a 170 X 1.8 Homodimer AB:CD AB CD - 4165 2211 1954
3GFI 146aa long hypothetical
transcriptional regulator		 S. tokodaii 146 X 2.1 Homodimer AC:DE AC DE - 742 379 364
3GNA V(D) J recombination-activating
protein 1		 M. musculus 96 X 2.4 Homodimer A:DE A DECF - 1602 838 764
3GXQ Putative regulator of transfer
genes ArtA		 S. aureus 54 X 2.4 Homodimer AB:CD AB CD - 1614 763 851
3GZ6 MutT/nudix family protein S. oneidensis 240 X 2.9 Homodimer AB:DC AB CD - 4338 2307 2031
3H0D CtsR G. stearothermophilus 155 X 2.4 Homodimer AB:DC AB CD - 3811 1925 1886
3HTS HEAT SHOCK TRANSCRIPTION FACTOR K. lactis 102 X 1.8 Homodimer B:A BD AC - 2362 1165 1197
3IGM PF14_0633 protein P. falciparum 77 X 2.2 Homodimer BA:WXCD AB CD - 1478 737 740
3IKT Redox-sensing transcriptional repressor rex T. thermophilus 207 X 2.3 Homodimer AB:CD AB CD - 3339 1684 1655
3IV5 DNA-binding protein fis E. coli 98 X 2.9 Homodimer AB:CD AB CD - 1957 1023 934
3JSO LexA repressor E. coli 202 X 2.3 Homodimer AB:CD AB CD - 3513 1618 1894
3KET Redox-sensing transcriptional repressor rex S. agalactiae
serotype III		 212 X 2.4 Homodimer A:BC AD BCEF - 1877 955 922
3KS8 Polymerase cofactor VP35 R. ebolavirus 184 X 2.4 Homo 2-mer ABCD:EF AB EF - 1663 799 864
3LSP DesT P. aeruginosa 220 X 2.7 Homodimer A:BD AC BD - 3041 1554 1487
3MLN Transcription factor COE1 M. musculus 224 X 2.4 Dimer ABE:CD AB CD - 5095 2632 2463
3MZH PROBABLE TRANSCRIPTIONAL REGULATORY
PROTEIN (PROBABLY CRP/FNR-FAMILY)		 M. tuberculosis 225 X 2.9 Homo 2-mer AB:CD AB CD - 2389 1191 1198
3N4M Catabolite gene activator +
DNA-directed RNA polymerase
subunit alpha		 E. coli 209+84 X 3.0 Hetero 6-mer ABC:DE A DE - 1374 685 689
3N4M Catabolite gene activator +
DNA-directed RNA polymerase
subunit alpha		 E. coli 209+84 X 3.0 Hetero 6-mer ABC:DE B DE - 771 360 411
3N4M Catabolite gene activator +
DNA-directed RNA polymerase
subunit alpha		 E. coli 209+84 X 3.0 Hetero 6-mer ABC:DE C DE - 819 380 439
3N7Q Transcription termination factor,
mitochondrial		 H. sapiens 310 X 2.4 Monomer A:BC A BC - 1261 639 622
3O9X Uncharacterized HTH-type
transcriptional regulator ygiT		 E. coli 133 X 2.1 Homo 2-mer AB:FE AB FE - 3059 1488 1571
3ON0 Protein traM E. coli 127 X 2.9 Homotetramer ABCD:P ABCD PI - 2340 1185 1155
3Q5F Transcriptional regulator slyA S. typhimurium 147 X 3.0 Homodimer AB:CD AB CD - 4205 2110 2095
3QMB CpG-binding protein H. sapiens 79 X 2.1 Monomer A:BC A BC - 1244 656 587
3R2C 30S ribosomal protein S10 +
N utilization substance protein B		 A. aeolicus 148+83 X 1.9 Heterodimer ABJK:RS AJ R - 2278 1027 1251
3RN2 Interferon-inducible protein AIM2 H. sapiens 208 X 2.6 Homo 2-mer AB:KL A KL - 1036 496 539
3RN2 Interferon-inducible protein AIM2 H. sapiens 208 X 2.6 Homo 2-mer AB:KL B KL - 1054 490 564
3TQ6 Transcription factor A,
mitochondrial		 H. sapiens 214 X 2.5 Monomer AB:CDEF A CD - 5353 2723 2630
3U3W C-terminus heptapeptide from PapR protein +
Transcriptional activator PlcR protein		 B. thuringiensis 293+7 X 2.4 Homodimer ABPQ:YZ AB YZ - 2576 1292 1283
3UGM TAL effector AvrBs3/PthA X. oryzae pv. oryzae 1047 X 3.0 Monomer A:BC A BC - 6201 2884 3317
3UGO RNA polymerase sigma factor T. aquaticus 245 X 2.1 Monomer A:B A B - 1882 882 999
3UK3 Zinc finger protein 217 H. sapiens 57 X 2.1 Homo 2-mer CD:AB C AB - 1658 865 794
3UK3 Zinc finger protein 217 H. sapiens 57 X 2.1 Homo 2-mer CD:AB D AB - 1535 802 733
3VOK Transcriptional regulator L. lactis
subsp. lactis		 189 X 2.0 Homodimer A:U AB UC - 1993 1000 993
3VWB Virulence regulon transcriptional
activator virB		 S. flexneri 143 X 2.4 Monomer A:CB A BC - 1432 731 701
3W6V AdpA S. griseus 147 X 3.0 Monomer A:BC A BC - 1545 752 793
3ZHM CI L. phage TP901-1 79 X 2.6 Monomer A:BC A BC - 1329 639 690
3ZKC HTH-TYPE TRANSCRIPTIONAL REGULATOR SINR B. subtilis 111 X 3.0 Homodimer AB:CD AB CD - 2675 1336 1339
3ZPL PUTATIVE MARR-FAMILY
TRANSCRIPTIONAL REPRESSOR		 S. coelicolor 177 X 2.8 Homodimer

ABEF:

CDGH

 AB CD - 3862 1894 1968
3ZPL PUTATIVE MARR-FAMILY
TRANSCRIPTIONAL REPRESSOR		 S. coelicolor 177 X 2.8 Homodimer

ABEF:

CDGH

 EF GH - 3825 1871 1954
3ZVK ANTITOXIN OF TOXIN-ANTITOXIN SYSTEM VAPB +
TOXIN OF TOXIN-ANTITOXIN SYSTEM		 R. felis 134+78 X 2.5 Hetero 8-mer

ABCDEFGH:

XY

 EH XY - 1863 936 928
3ZVK ANTITOXIN OF TOXIN-ANTITOXIN SYSTEM VAPB +
TOXIN OF TOXIN-ANTITOXIN SYSTEM		 R. felis 134+78 X 2.5 Hetero 8-mer

ABCDEFGH:

XY

 FG XY - 1873 938 935
4EGY Arabinose metabolism
transcriptional repressor		 B. subtilis 88 X 2.3 Monomer AB:TU A TU - 1861 966 895
4EGY Arabinose metabolism
transcriptional repressor		 B. subtilis 88 X 2.3 Monomer AB:TU B TU - 1796 927 869
4F6M Transcriptional regulator Kaiso H. sapiens 133 X 2.4 Monomer A:DE A DE - 2706 1390 1315
4G7H DNA-directed RNA polymerase subunit alpha +
DNA-directed RNA polymerase subunit beta +
DNA-directed RNA polymerase subunit beta' +
DNA-directed RNA polymerase subunit omega +
RNA polymerase sigma factor		 T. thermophilus

1119+1524

+315+443

+99

 X 2.9 Hetero 6-mer

ABCD

EFKL

MNOP:

GHQR

 D GH - 1888 957 931
4G7H DNA-directed RNA polymerase subunit alpha +
DNA-directed RNA polymerase subunit beta +
DNA-directed RNA polymerase subunit beta' +
DNA-directed RNA polymerase subunit omega +
RNA polymerase sigma factor		 T. thermophilus

1119+1524+

315+443+99

 X 2.9 Hetero 6-mer

ABCD

EFKL

MNOP:

GHQR

 F GH - 2562 1170 1392
4G92 HAPB protein +
HapE +
Transcription factor HapC (Eurofung)		 E. nidulans 119+64+92 X 1.8 Hetero 3-mer ABC:DE A DE - 1950 1029 921
4G92 HAPB protein +
HapE +
Transcription factor HapC (Eurofung)		 E. nidulans 119+64+92 X 1.8 Hetero 3-mer ABC:DE B DE - 938 437 501
4G92 HAPB protein +
HapE +
Transcription factor HapC (Eurofung)		 E. nidulans 119+64+92 X 1.8 Hetero 3-mer ABC:DE C DE - 988 457 532
4H10 Polymerase cofactor VP35 H. sapiens 146 X 2.4 Heterodimer AB:CD AB CD - 2406 1270 1137
4HF1 Aryl hydrocarbon receptor nuclear
translocator-like protein 1 +
Circadian locomoter output cycles protein kaput		 E. coli 71+73 X 2.2 Homodimer AB:CD AB CD - 3790 1886 1904
4HLY K9 H. herpesvirus
8 type P		 132 X 1.5 Homo 2-mer AB:CD AB CD - 938 463 474
4HQE Transcriptional regulator QsrR S. aureus 115 X 2.3 Homodimer AB:CD AB CD - 2483 1215 1268
4HQU Platelet-derived growth factor subunit B H. sapiens 109 X 2.2 Homodimer A:C AB CD - 314 132 182
4I2O FixK2 protein B. japonicum 243 X 1.8 Homodimer AB:WX AB WX - 2546 1240 1307
4IHT HTH-type transcriptional regulator BenM A. baylyi 94 X 3.0 Homodimer

ABCD:

EFGH

 AB EF - 3408 1722 1686
4IQR Hepatocyte nuclear factor 4-alpha +
Nuclear receptor coactivator 2		 H. sapiens 13+338 X 2.9 Homodimer

ABEFIJKL:

CDGH

 AB CD - 3434 1653 1780
4IZZ Transcription Factor HetR F. thermalis 302 X 2.5 Homodimer AB:CD AB CD - 2957 1463 1494
4J19 Homeobox-containing protein 1 H. sapiens 113 X 2.9 Monomer AB:CD A CD - 1294 681 614
4J19 Homeobox-containing protein 1 H. sapiens 113 X 2.9 Monomer AB:CD B CD - 1960 1043 918
4J2X Four and a half LIM domains protein 1 +
Recombining binding protein suppressor of hairless		 M. musculus 28+427 X 2.9 Monomer

ABCD:

EFGH

 A GH - 2203 1117 1086
4JCX Csp231I C protein C. sp. RFL231 98 X 2.3 Homodimer AB:CD AB CD - 2735 1365 1370
4JL3 Transcriptional regulator, TetR family M. smegmatis 196 X 2.5 Homodimer ABCD:EF AB EF - 2501 1264 1237
4JL3 Transcriptional regulator, TetR family M. smegmatis 196 X 2.5 Homodimer ABCD:EF CD EF - 3202 1636 1566
4KFC KDP operon transcriptional regulatory protein KdpE E. coli 227 X 2.5 Homodimer AB:YZ AB YZ - 2985 1422 1564
4LDX Auxin response factor 1 A. thaliana 363 X 2.9 Homodimer AB:CD AB CD - 3550 1810 1740
4LLN MepR S. aureus 140 X 2.8 Homodimer

ABCDIJ:

GHEFKL

 AB GH - 4025 1951 2075
4LMG Iron-regulated transcriptional
activator AFT2		 S. cerevisiae 157 X 2.2 Monomer ABCD:EFGH ABCD EFGH - 5803 2830 2973
4LUP RNA polymerase sigma factor E. coli 106 X 1.2 Monomer AC:BD A B - 1288 590 698
4M8B YHR177W S. cerevisiae 202 X 2.6 Monomer R:AB R AB - 2162 1094 1068
4MTD Zinc uptake regulation protein E. coli 171 X 2.5 Homodimer ABCD:YZ AB YZ - 2868 1384 1484
4MTD Zinc uptake regulation protein E. coli 171 X 2.5 Homodimer ABCD:YZ CD YZ - 3110 1584 1526
4NHJ DNA-binding transcriptional regulator RstA K. pneumoniae
subsp. pneumoniae		 119 X 2.7 Homodimer AB:CD AB CD - 3236 1670 1566
4ON0 NolR R. fredii 118 X 3.0 Homodimer ABCD:EGFH AB EF - 2982 1489 1492
4PZI Histone-lysine N-methyltransferase 2B H. sapiens 67 X 2.2 Monomer A:BC A BC - 1705 877 827
4QTJ White-opaque regulator 1 C. albicans 274 X 2.1 Monomer A:BC A BC - 1513 768 745
4R22 HTH-type transcriptional
regulator TnrA		 P. megaterium 82 X 2.6 Homodimer B:G AB CG - 3016 1440 1577
4RB1 DNA-binding transcriptional dual
regulator of siderophore
biosynthesis and transport(Fur family)		 M. gryphiswaldense 145 X 2.8 Homodimer AB:D AB DF - 2801 1418 1382
4RB1 DNA-binding transcriptional dual
regulator of siderophore biosynthesis
and transport(Fur family)		 M. gryphiswaldense 145 X 2.8 Homodimer AB:D CE DF - 2801 1418 1382
4ROC TATA-box-binding protein + Transcription factor IIIB 50 kDa subunit H. sapiens 183+360 X 1.9 Hetero dimer AB:NT A NT - 2170 1059 1111
4ROC TATA-box-binding protein + Transcription factor IIIB 50 kDa subunit H. sapiens 183+360 X 1.9 Hetero dimer AB:NT B NT - 2921 1452 1469
4UX5 TRANSCRIPTION FACTOR MBP1 P. oryzae 136 X 2.4 Monomer AB:CD A CD - 1587 806 781
4UX5 TRANSCRIPTION FACTOR MBP1 P. oryzae 136 X 2.4 Monomer AB:CD B CD - 1369 693 676
4WLS HTH-type transcriptional regulator CueR E. coli 128 X 2.1 Homodimer AB:XYUV AB XY - 2864 1400 1465
4WU4 Response regulator receiver domain protein NA 68 X 2.3 Homodimer AB:GH AB GH - 2159 1048 1112
4XRM Homeobox protein Meis2 H. sapiens 64 X 1.6 Monomer AB:ML A ML - 1223 627 595
4XRM Homeobox protein Meis2 H. sapiens 64 X 1.6 Monomer AB:ML B ML - 1246 642 604
4Y00 TAR DNA-binding protein 43 H. sapiens 103 X 3.0 Monomer

ABCD:

EFGH

 A E - 1455 663 792
4Z3C Methylcytosine dioxygenase H. sapiens 52 X 1.6 Monomer C:AB C AB - 1349 702 647
5D23 Fibroin-modulator-binding protein-1 B. mori 102 X 2.0 Monomer A:B A B - 2412 1263 1149
5D8C MerR family regulator protein H. influenzae 137 X 2.3 Homodimer AB:CD AB CD - 2618 1257 1361
5DY0 TetR family transcriptional regulator C. glutamicum 230 X 3.0 Homodimer

ABCD:

EFGH

 AB EF - 3308 1674 1634
5EG6 Recombining binding protein suppressor of hairless+hRITA M. musculus 16+422 X 2.1 Hetero 2-mer CR:BA C AB - 1421 709 712
5EYB DNA-binding protein reb1 S. pombe 362 X 2.7 Monomer AB:CDEF AB CDEF - 8802 4334 4468
5F7Q Lmo0178 protein L. monocytogenes serovar 1/2a 407 X 2.4 Homodimer CEJL:FK CE FK - 4532 2348 2184
5FD3 Protein lin-54 homolog H. sapiens 135 X 2.4 Monomer AB:CDHI AB CDHI - 4010 1909 2101
5FMP HTH-TYPE TRANSCRIPTIONAL REPRESSOR KSTR M. tuberculosis 205 X 2.3 Homodimer AB:CD AB CD - 2283 1129 1155
5GNJ Transcription factor MYC2 A. thaliana 89 X 2.7 Homodimer

GIAB

EFMN:

KLCD

HJOP

 GI KL - 2156 1122 1034
5GPC Transcriptional regulator (TetR/AcrR family) H. halodurans 194 X 2.8 Homodimer ABCD:GE AB EG - 2188 1073 1115
5GPC Transcriptional regulator (TetR/AcrR family) H. halodurans 194 X 2.8 Homodimer ABCD:GE CD EG - 2171 1054 1117
5GZB Transcriptional enhancer factor TEF-3 H. sapiens 107 X 2.7 Monomer A:BC A BC - 2061 1057 1005
5H3R Multiple antibiotic resistance protein MarR E. coli 147 X 2.7 Homodimer AB:CD AB CD - 3489 1741 1748
5HLG MarR family transcriptional regulator S. epidermidis 148 X 3.0 Homodimer

ABCDEFGH:

IJKLMNOP

 AB IJ - 3944 1944 2000
5HSO Uncharacterized HTH-type transcriptional regulator Rv2887 M. tuberculosis 160 X 2.5 Homodimer ABCD:EF AB EF - 798 411 387
5HSO Uncharacterized HTH-type transcriptional regulator Rv2887 M. tuberculosis 160 X 2.5 Homodimer ABCD:EF CD EF - 938 471 467
5I44 Chromosome-anchoring protein RacA B. subtilis 69 X 2.6 Homodimer

BADE

GFHIJK:

UTZRPW

 ABDE UW - 4158 2082 2076
5J2Y Regulatory protein P. aeruginosa 80 X 2.4 Monomer AB:FR A F - 645 328 317
5J3E Thymocyte nuclear protein 1 H. sapiens 225 X 2.6 Monomer AB:CDEF A EF - 1069 519 551
5JGH ARS-binding factor 2, mitochondrial S. cerevisiae 163 X 2.6 Monomer

ADGJ:

BCEFHIKL

 A BCEF - 4528 2323 2204
5JGH ARS-binding factor 2, mitochondrial S. cerevisiae 163 X 2.6 Monomer

ADGJ:

BCEFHIKL

 D BCEF - 4385 2224 2161
5JLT Middle transcription regulatory protein motA E. phage T4 125 X 3.0 Monomer

ABCD:

EFGH

 A EF - 2025 1030 995
5JUB ComS+Transcriptional regulator S. thermophilus 310+8 X 2.6 Homodimer ABCD:XZ AB XZ - 2275 1092 1182
5K5Q AspA S. sp. NOB8H2 92 X 2.7 Homodimer CDABEF:PN CD PN - 2948 1508 1440
5K5Q AspA S. sp. NOB8H2 92 X 2.7 Homodimer CDABEF:PN AB PN - 3260 1631 1629
5K5Q AspA S. sp. NOB8H2 92 X 2.7 Homodimer CDABEF:PN EF PN - 2793 1415 1378
5K7Z Transcriptional regulator, TetR family M. xanthus 231 X 2.9 Homo 2-mer ABCD:EF AB EF - 2313 1151 1161
5LEJ Listeriolysin regulatory protein L. monocytogenes serovar 1/2a 237 X 2.7 Homodimer AB:CD AB CD - 2735 1345 1390
5LXU Transcription factor LUX A. thaliana 57 X 2.1 Monomer A:UB A BU - 1363 682 681
5MHJ Major viral transcription factor ICP4 H. herpesvirus 1 201 X 2.1 Homodimer AB:EF AB EF - 1630 862 768
5MPF Grainyhead-like protein 1 homolog H. sapiens 238 X 2.9 Homodimer AB:EF AB EF - 2595 1364 1231
5OND Transcription antitermination protein RfaH E. coli 162 X 2.1 Monomer AB:CD A C - 863 376 487
5TW1 DNA-directed RNA polymerase subunit alpha +
DNA-directed RNA polymerase subunit beta +
DNA-directed RNA polymerase subunit beta' +
DNA-directed RNA polymerase subunit omega +
RNA polymerase sigma factor SigA +
RNA polymerase-binding protein RbpA +
Unknown peptide		 M. smegmatis

107+114+1169

+1317+17+350

+466

 X 2.8 Hetero 9-mer

JABC

DEFT:

OP

 C OP - 9 5 4
5TW1 DNA-directed RNA polymerase subunit alpha +
DNA-directed RNA polymerase subunit beta +
DNA-directed RNA polymerase subunit beta' +
DNA-directed RNA polymerase subunit omega +
RNA polymerase sigma factor SigA +
RNA polymerase-binding protein RbpA +
Unknown peptide		 M. smegmatis

107+114+1169

+1317+17+

350+466

 X 2.8 Hetero 9-mer

JABC

DEFT:

OP

 D OP - 227 108 118
5TW1 DNA-directed RNA polymerase subunit alpha +
DNA-directed RNA polymerase subunit beta +
DNA-directed RNA polymerase subunit beta' +
DNA-directed RNA polymerase subunit omega +
RNA polymerase sigma factor SigA +
RNA polymerase-binding protein RbpA +
Unknown peptide		 M. smegmatis

107+114+1169

+1317+17+350

+466

 X 2.8 Hetero 9-mer

JABC

DEFT:

OP

 F OP - 3866 1915 1951
5TW1 DNA-directed RNA polymerase subunit alpha +
DNA-directed RNA polymerase subunit beta +
DNA-directed RNA polymerase subunit beta' +
DNA-directed RNA polymerase subunit omega +
RNA polymerase sigma factor SigA +
RNA polymerase-binding protein RbpA +
Unknown peptide		 M. smegmatis

107+114+1169

+1317+17+350

+466

 X 2.8 Hetero 9-mer

JABC

DEFT:

OP

 J OP - 167 84 83
5TW1 DNA-directed RNA polymerase subunit alpha +
DNA-directed RNA polymerase subunit beta +
DNA-directed RNA polymerase subunit beta' +
DNA-directed RNA polymerase subunit omega +
RNA polymerase sigma factor SigA +
RNA polymerase-binding protein RbpA +
Unknown peptide		 M. smegmatis

107+114+1169

+1317+17+350

+466

 X 2.8 Hetero 9-mer

J JABC

DEFT:

OP

 T OP - 809 389 421
5VL9 Regulatory protein TetR E. lignolyticus 192 X 2.2 Homodimer

ABCD:

EFGH

 AB EFGH - 2471 1277 1194
5WX9 Ethylene-responsive transcription factor ERF096 A. thaliana 131 X 1.8 Monomer A:BC A BC - 2612 1357 1256
5X11 Transcriptional regulator B. spizizenii 188 X 2.7 Homodimer

ABCDEFGH:

IJMN

 AB IJ - 4222 2121 2101
5X5L AdeR A. baumannii 109 X 2.8 Homo 6-mer

ABEHMN:

CDFG

 BH CD - 3582 1766 1816
5XFP PHD finger protein 1 H. sapiens 336 X 2.3 Monomer ABE:CD B CD - 1011 526 485
5XFQ PHD finger protein 1 +
Peptide from Histone H3		 M. musculus 13+336 X 2.4 homo 2-mer ABEF:CD A CD - 994 505 489
5XSK Hepatoma-derived growth factor R. norvegicus 120 X 2.8 Homodimer AB:DF AB DF - 720 335 385
5YEJ TetR family transcriptional regulator M. smegmatis 232 X 2.7 Homodimer ABC:DFG BC DF - 2863 1407 1456
5YI2 Zinc transport transcriptional regulator L. lactis subsp. lactis 146 X 2.6 Homodimer

ABEF

IJMN:

CGKO

DPLH

 AB CD - 2596 1310 1286
5ZD4 Maltose-binding periplasmic protein,
Protein BRASSINAZOLE-RESISTANT 1		 A. thaliana 453 X 2.2 Homodimer

CDAB:

GHEF

 CD GH - 3065 1560 1505
5ZGN KacA + KacT K. pneumoniae
subsp. pneumoniae		 177+88 X 2.2 Hetero 6-mer ABCDEF:GH ABCDEF GH - 3687 1865 1822
6ASB F-box/LRR-repeat protein 19 H. sapiens 123 X 2.9 Monomer

CFIL:

ABDE

GHJK

 A BC - 1707 888 820
6C2S Transcriptional regulator,
MarR family		 R. palustris 186 X 2.9 Homodimer

ABCD:

UVXY

 AD UV - 3000 1511 1490
6C31 TetR family transcriptional regulator M. tuberculosis 214 X 3.0 Homodimer

ABCD

EFGH:

IJKL

 AD KL - 3017 1494 1523
6C31 TetR family transcriptional regulator M. tuberculosis 214 X 3.0 Homodimer

ABCD

EFGH:

IJKL

 BC KL - 2536 1257 1279
6CG8 UPF0335 protein B7Z12_12435 C. vibrioides 78 X 2.3 Homodimer ABDE:CF ABDE CF - 1395 684 711
6CHV Antitoxin HigA P. vulgaris 121 X 2.9 Homodimer

ACBD

GH:

IJEFKL

 AC IJ - 2582 1288 1294
6CRO LAMBDA CRO REPRESSOR E. phage lambda 60 X 3.0 Homodimer A:RU AB RUCD - 1397 735 661
6EL8 Forkhead box protein N1 H. sapiens 99 X 1.6 Monomer

AD:

BCEF

 A BC - 1481 755 726
6FAS B3 domain-containing transcription
repressor VAL1		 A. thaliana 119 X 1.9 Monomer

AB:

CDEF

 A CD - 1386 691 695
6FN0 Cryptochrome photoreceptor C. reinhardtii 499 X 2.9 Monomer A:CD A CD - 1861 902 959
6G1T AM32 E. faecalis 122 X 1.9 Monomer A:ED A DE - 3231 1599 1633
6HP7 SPBc2 prophage-derived
uncharacterized protein YopK		 B. subtilis 386 X 2.2 Homodimer AB:CD AB CD - 4010 1925 2085
6IDE Transcriptional regulator LuxR family V. cholerae 256 X 2.5 Homodimer AB:CD AB CD - 2586 1285 1301
6IR8 OsWRKY45 O. sativa subsp. japonica 69 X 2.3 Monomer A:BC A BC - 1218 615 603
6J4F Probable WRKY transcription factor 2 A. thaliana 82 X 2.4 Monomer

BF:

CDGH

 B CD - 1259 619 641
6JBX Fatty acid biosynthesis transcriptional
regulator		 S. pneumoniae 152 X 2.2 Homodimer AB:CD AB CD - 3613 1762 1851
6JGW CadR P. putida 147 X 2.8 Homodimer BA:CD AB CD - 3043 1431 1612
6LB3 HTH cro/C1-type domain-containing protein P. aeruginosa 109 X 2.5 Homo 4-mer

ABCD

EFGH:

IJKLMN

 AB IJ - 1652 800 853
6LUI Atherin H. sapiens 80 X 1.8 Monomer A:BC A BC - 1534 794 740
6LXN Transcriptional regulatory protein OmpR E. coli 113 X 2.9 Homodimer AB:CD AB CD - 3424 1712 1711
6MRJ Nickel-responsive regulator H. pylori 148 X 2.8 Homo 4-mer

ABCD:

LM

 AB LM - 1764 887 877
6MRJ Nickel-responsive regulator H. pylori 148 X 2.8 Homo 4-mer ABCD:LM CD LM - 2055 1014 1041
6NSM TetR family transcriptional regulator CifR P. aeruginosa 198 X 2.8 Homodimer AB:CD AB CD - 3617 1886 1730
6ON0 Gp39 R. N15 71 X 1.6 Homodimer AB:CN AB CN - 1977 997 980
6P0S DNA-binding protein Fis +
Excisionase		 E. phage lambda 55+98 X 2.7 FiS Homodimer and
Excisionase Monomer		 ABE:CD ABE CD - 3543 1797 1745
6P1A Q protein E. phage 21 162 X 2.8 Homo 2-mer

ABC:

DEFG

 C FG - 1680 875 805
6P1A Q protein E. phage 21 162 X 2.8 Homo 2-mer

ABC:

DEFG

 B DE - 1724 918 807
6P1A Q protein E. phage 21 162 X 2.8 Homo 2-mer

ABC:

DEFG

 A DE - 1708 898 811
6Q2B MarR family transcriptional regulator L. monocytogenes
serovar 1/2a		 153 X 2.7 Homodimer AB:CD AB CD - 4511 2277 2234
6QFD DNA-binding protein H. salinarum 116 X 2.1 Hetero 2-mer

ABCD:

EFGH

 AB EF - 3484 1715 1770
6RYD Protein WUSCHEL A. thaliana 76 X 1.6 Homodimer

ABEF:

CDGH

 EF GH - 3016 1576 1440
6W1A Transcriptional regulator S. dysgalactiae 284 X 2.8 Homodimer AB:EF AB EF - 2465 1203 1262
6ZA3 Transcriptional regulator,
GntR family		 A. fabrum 250 X 2.1 Homodimer AB:EF AB EF - 2214 1075 1139
7AMN HTH-type transcriptional
regulator LuxR		 V. alginolyticus 221 X 2.3 Homodimer BA:EF BA EF - 3488 1752 1736
7B0C HTH-type transcriptional
repressor NsrR		 S. coelicolor 161 X 3.0 Homodimer AB:CD AB CD - 3469 1743 1726
7BCB KORA domain-containing protein E. coli 110 X 2.8 Homodimer AB:CD AB CD - 2317 1173 1144
7BHY Deoxyribonucleoside regulator B. subtilis 57 X 2.3 Homodimer ABC:EG AB EG - 1829 945 884
7BZG HTH-type transcriptional activator HxlR B. subtilis 123 X 2.9 Homodimer

ABEFIJ:

CDGHKL

 AB CD - 2943 1400 1543
7C0G Aca1 P. phage 79 X 2.4 Homo 2-mer AB:CD AB CD - 951 497 454
7C9O Nuclear transcription factor Y subunit B-11 +
Nuclear transcription factor Y subunit C-2 +
Zinc finger protein HD1		 O. sativa subsp. japonica 104+67+95 X 2.6 trimer ABC:DE ABC DE - 3464 1680 1784
7DVV HTH marR-type domain-containing protein S. agalactiae serotype III 153 X 2.5 Homodimer AB:LM AB LM - 4640 2313 2326
7EL3 Homoprotocatechuate degradation
operon regulator HpaR		 A. baumannii 141 X 1.7 Homodimer AB:CD AB CD - 4273 2152 2121
7EOF Coiled-coil domain-containing protein 25 H. sapiens 204 X 2.7 Homo 2-mer BA:CD AB CD - 376 196 180
7ET4 AP2/ERF and B3 domain-containing
transcription repressor TEM1		 A. thaliana 122 X 2.7 Monomer

ADGJ:

BCEFHIKL

 A BC - 1608 792 816
7ET6 AP2/ERF and B3 domain-containing
transcription repressor TEM1		 A. thaliana 125 X 2.7 Monomer DA:EF A EF - 1846 908 938
7ET6 AP2/ERF and B3 domain-containing
transcription repressor TEM1		 A. thaliana 125 X 2.7 Monomer DA:EF D EF - 720 316 404
7F2F Serine-rich protein TYE7 S. cerevisiae 136 X 2.6 Homodimer AB:EH AB EH - 2904 1444 1460
7F9H EnrR repressor E. piscicida 90 X 1.8 Monomer AB:CD A CD - 1565 747 818
7F9H EnrR repressor E. piscicida 90 X 1.8 Monomer AB:CD B CD - 1607 777 831
7JNP HTH-type transcriptional regulator MtrR N. gonorrhoeae 213 X 2.6 Homodimer AB:CD AB CD - 2366 1172 1194
7LH9 Bromodomain-containing protein 1 H. sapiens 126 X 2.6 Monomer

ABCD:

EFGHIJKL

 A EFBC - 1426 715 711
7PRV Glucocorticoid receptor +
Peroxisome proliferator-activated receptor
gamma coactivator 1-alpha		 H. sapiens 21+393 X 2.7 Homodimer ABF:CD AB CD - 2622 1302 1320
7PZA Putative cAMP-binding protein-catabolite
gene activator		 R. meliloti 244 X 2.7 Homodimer

AB:

CDEF

 AB CDEF - 2506 1259 1247
7T8K BrxR A. sp. NEB 394 291 X 2.3 Homodimer AB:CD AB CD - 3192 1610 1582
7TZ1 Immunity repressor M. phage TipsytheTRex 203 X 2.8 Monomer A:BC A BC - 3120 1567 1554
7V6W Antitoxin+Putative mRNA
interferase YoeB		 S. aureus 85+89 X 2.6 Homodimer

FBCA

EMLI

KNDJ:

GHPO

 AB GH - 1834 918 916
7V6W Antitoxin+Putative mRNA
interferase YoeB		 S. aureus 85+89 X 2.6 Homodimer

FBCA

EMLI

KNDJ:

GHPO

 CD GH - 1816 926 890
7V9F BEN domain-containing protein 3 M. musculus 114 X 2.5 Monomer A:BC A BC - 579 261 318
7VJQ anti-CRISPR-associated protein Aca2 P. phage ZF40 121 X 2.8 Homodimer AB:CD AB CD - 2268 1175 1093
7VP1 Transcription factor TCP10 A. thaliana 107 X 2.9 Homo 2-mer AB:CD AB CD - 2408 1224 1184
7X5G Nuclear factor erythroid 2-related factor 2 +
Transcription factor MafG		 H. sapiens 104+113 X 2.3 Heterodimer

ABEF:

CDGH

 AB CD - 2771 1423 1348
7XQ5 Protein INO2 +
Protein INO4		 S. cerevisiae 73+75 X 2.3 Heterodimer AB:CD AB CD - 3239 1649 1590
7YUK Protein BANP H. sapiens 141 X 2.1 Monomer A:CD A CD - 1338 658 680
7YZG Forkhead box protein H1 X. laevis 140 X 2.8 Monomer A:BC A BC - 2363 1168 1195
7ZG5 Acetyltransferase +
DUF1778 domain-containing protein		 S. typhimurium 176+94 X 2.0 Homodimer ABCD:EF CD EF - 534 264 270
8B4B Cholera toxin transcriptional activator V. cholerae serotype O1 110 X 1.8 Monomer tandem repeat

WXYZ:

LM

 W LM - 1344 645 699
8B4B Cholera toxin transcriptional activator V. cholerae serotype O1 110 X 1.8 Monomer tandem repeat

WXYZ:

LM

 X LM - 988 490 499
8B4B Cholera toxin transcriptional activator V. cholerae serotype O1 110 X 1.8 Monomer tandem repeat

WXYZ:

LM

 Z LM - 1654 815 839
8B4B Cholera toxin transcriptional activator V. cholerae serotype O1 110 X 1.8 Monomer tandem repeat

WXYZ:

LM

 Y LM - 1005 497 508
8EB5 Hermes transposase BED domain M. domestica 78 X 2.5 Monomer, two repeat A:CD AB CE - 3163 1569 1594
8EJO Homeobox domain-containing protein O. anatinus 71 X 2.7 Homodimer AB:CD B CD - 1866 961 905
8HML DNA-binding response OmpR family regulator S. erythraea 143 X 3.0 Monomer tandem repeat AB:DC A CD - 1476 731 744
8HML DNA-binding response OmpR family regulator S. erythraea 143 X 3.0 Monomer tandem repeat AB:DC B CD - 1764 878 885
8IKE LMX1A factor H. sapiens 60 X 2.6 Monomer C:AB C AB - 1537 750 787
8J0K Transcription factor AP-2-alpha H. sapiens 219 X 2.1 Homodimer AB:CD AB CD - 2263 1156 1107
8K4L Nuclear respiratory factor 1 H. sapiens 109 X 2.3 Homodimer A:C AB CD - 3068 1506 1562
8K86 Nuclear factor
interleukin-3-regulated protein		 H. sapiens 73 X 2.1 Homodimer AB:CD AB CD - 2481 1283 1198
8P5Q Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 3 A. thaliana 129 X 2.1 Monomer A:BC A BC - 2121 1054 1067
8PW0 Iron dependent repressor,
putative		 D. radiodurans 148 X 2.2 Homodimer A:B AC BD - 3276 1652 1624
8UVK DNA-binding response regulator C. jejuni 224 X 2.2 Homodimer AB:CD AB CD - 2781 1392 1389
8YEY Activating signal cointegrator 1 H. sapiens 148 X 2.0 Monomer CA:DB A B - 501 242 259
1A66 CORE NFATC1 H. sapiens 178 N - Monomer A:BC A BC - 2213 1085 1128
1AHD Homeotic protein antennapedia D. melanogaster 68 N - Monomer P:AB P AB - 2290 1159 1130
1C7U MYOCYTE-SPECIFIC ENHANCER FACTOR 2A,
C4 FORM		 H. sapiens 85 N - Homodimer AB:CD AB CD - 3490 1807 1683
1CJG PROTEIN (LAC REPRESSOR) E. coli 62 N - Homodimer AB:CD AB CD - 3780 1832 1948
1CO0 TRP OPERON REPRESSOR E. coli 107 N - Homodimer AB:EF AB EF - 3006 1516 1491
1F4S ETHANOL REGULON TRANSCRIPTIONAL FACTOR E. nidulans 65 N - Monomer P:AB P AB - 2211 1162 1049
1G4D REPRESSOR PROTEIN C E. phage Mu 69 N - Monomer A:BC A BC - 1708 888 819
1GAT ERYTHROID TRANSCRIPTION
FACTOR GATA-1		 G. gallus 60 N - Monomer A:BC A BC - 2036 1039 997
1GCC ETHYLENE RESPONSIVE ELEMENT
BINDING FACTOR 1		 A. thaliana 63 N - Monomer A:BC A BC - 1612 832 780
1HRY HUMAN SRY H. sapiens 76 N - Monomer A:BC A BC - 2106 1136 971
1J4W FUSE binding protein H. sapiens 174 N - Monomer A:B A B - 2045 994 1052
1KQQ DEAD RINGER PROTEIN D. melanogaster 139 N - Monomer A:BC A BC - 1745 863 882
1LFU homeobox protein PBX1 M. musculus 82 N - Monomer P:AB P AB - 2210 1178 1032
1LO1 Steroid hormone receptor ERR2 H. sapiens 98 N - Monomer A:BC A BC - 2452 1245 1208
1MSE C-Myb DNA-Binding Domain M. musculus 105 N - Monomer C:AB C AB - 2841 1358 1483
1O4X Transcription factor SOX-2 +
transcription factor Oct-1		 H. sapiens 167+88 N - Heterodimer AB:CD AB CD - 4894 2516 2379
1TF3 TRANSCRIPTION FACTOR IIIA X. laevis 92 N - Monomer A:EF A EF - 3255 1638 1616
1XS9 DNA-directed RNA polymerase alpha chain +
Multiple antibiotic resistance protein marA		 E. coli 132+84 N - Monomer AD:BC AD BC - 2795 1407 1388
1YUI GAGA-FACTOR D. melanogaster 54 N - Monomer A:BC A BC - 2359 1243 1116
1ZGW Ada polyprotein E. coli 139 N - Monomer A:BC A BC - 2457 1242 1214
2HDC TRANSCRIPTION FACTOR R. norvegicus 97 N - Monomer A:BC A BC - 2375 1185 1190
2JX1 Myelin transcription factor 1 M. musculus 31 N - Monomer A:BC A BC - 1419 754 666
2K1N AbrB family transcriptional regulator B. subtilis 55 N - Homo 2-mer ABCD:EF AB EF - 1731 828 903
2K1N AbrB family transcriptional regulator B. subtilis 55 N - Homo 2-mer ABCD:EF CD EF - 1423 659 765
2KAE GATA-type transcription factor C. elegans 71 N - Monomer A:BC A BC - 2962 1585 1376
2KKF Histone-lysine N-methyltransferase HRX H. sapiens 59 N - Monomer A:BC A BC - 1904 1009 894
2KMK Zinc finger protein Gfi-1 R. norvegicus 82 N - Monomer A:BC A BC - 2762 1430 1331
2KO0 THAP domain-containing protein 1 H. sapiens 87 N - Monomer A:BC A BC - 2171 1141 1030
2LEF LYMPHOID ENHANCER-BINDING FACTOR M. musculus 86 N - Monomer A:BC A BC - 3677 1884 1793
2LEV Ler E. coli 57 N - Monomer A:BC A BC - 928 454 474
2LEX Probable WRKY transcription factor 4 A. thaliana 78 N - Monomer A:BC A BC - 1200 591 609
2MAP RNA polymerase sigma factor E. coli 96 N - Monomer A:B A B - 1433 665 768
2MRU Antitoxin MazE E. coli 67 N - Homodimer AB:XY AB XY - 1675 865 810
2MXF MvaT P. aeruginosa 55 N - Monomer A:BC A BC - 1637 851 785
2O8K RNA polymerase sigma factor RpoN A. aeolicus 63 N - Monomer A:BC A BC - 1553 745 808
2P7C Penicillinase repressor B. licheniformis 82 N - Monomer B:AC B AC - 2320 1099 1222
2STT ETS1 H. sapiens 96 N - Monomer A:BC A BC - 1815 907 907
2Z33 Phosphate regulon transcriptional
regulatory protein phoB		 E. coli 104 N - Monomer A:BC A BC - 1968 979 989
II. RNA-binding Transcription Factors
1C9S TRP RNA-BINDING ATTENUATION PROTEIN G. stearothermophilus 74 X 1.9 Homo 11-mer

ABCD

EFGH

IJKLM

NOPQ

RST

UV:W

 L W 1050 502 548
1WMQ Hut operon positive regulatory protein B. subtilis 147 X 1.6 Homo 6-mer AB:CD AB C 1448 653 795
2A8V RNA BINDING DOMAIN OF RHO
TRANSCRIPTION TERMINATION FACTOR		 E. coli 118 X 2.4 Monomer ABC:DE B E 719 281 438
2ASB Transcription elongation protein nusA M. tuberculosis 251 X 1.5 Monomer A:B A B 2316 1092 1225
4GHA Polymerase cofactor VP35 O. marburgense 146 X 2.5 Homo 4-mer ACEG:IJ A IJ 1016 489 527
4GHA Polymerase cofactor VP35 O. marburgense 146 X 2.5 Homo 4-mer ACEG:IJ C IJ 700 339 360
4GHA Polymerase cofactor VP35 O. marburgense 146 X 2.5 Homo 4-mer ACEG:IJ E IJ 1025 495 530
4GHA Polymerase cofactor VP35 O. marburgense 146 X 2.5 Homo 4-mer ACEG:IJ G IJ 1040 505 535
5M3H Polymerase acidic protein +
Polymerase basic protein 2 +
RNA-directed RNA polymerase catalytic subunit +
TYR-SER-PRO-THR-SEP-PRO		 H. sapiens

28+728+

776+797

 X 2.5 Hetero 5-mer ABCXY:RV ABC RV 5352 2563 2789
6FHI Polymerase acidic protein +
Polymerase basic protein 2 +
RNA-directed RNA polymerase catalytic subunit +
TYR-SER-PRO-THR-SEP-PRO-SER-TYR-SER-PRO-SER-TYR-
SER-PRO-THR-SEP-PRO-SER-TYR		 H. sapiens,
Influenza A virus

19+738+

776+809

 X 2.8 Hetero 4-mer ABCX:RV ABC RV 5460 2627 2833
8F5G Transcription termination/
antitermination protein NusG		 T. pseudethanolicus 182 X 2.7 Monomer ABC:DEF A D 1529 751 778
1L1C Transcription antiterminator licT B. subtilis 55 N - Homo 2-mer AB:C AB CD 2352 1168 1184
1QFQ 36-mer N-terminal peptide of the N protein E. phage lambda 35 N - Monomer B:A B A 1322 674 648
III. DNA/RNA-binding Transcription Factors
5XOG DNA-directed RNA polymerase subunit +
DNA-directed RNA polymerase subunit +
DNA-directed RNA polymerase subunit beta +
RNA polymerase II subunit +
RNA polymerase II subunit B12.5 +
RNA polymerase II subunit B32 +
RNA polymerase II third largest subunit B44 +
RNA polymerase subunit ABC10-alpha +
RNA polymerase subunit ABC14.5 +
RNA polymerase subunit ABC23 +
RNA polymerase subunit ABC27 +
Spt4/5 complex component +
Transcription elongation factor 1 homolog		 K. phaffii

115+118+1227

+145+155+171

+1743+186+214

+304+72+83+85

 X 3.0 Hetero 14-mer

ABCD

EFGH

IJKLM

W:TN

 ABE NT 4263 2089 2174
5ZX2 DNA-directed RNA polymerase subunit alpha +
DNA-directed RNA polymerase subunit beta +
DNA-directed RNA polymerase subunit beta' +
DNA-directed RNA polymerase subunit omega +
ECF RNA polymerase sigma factor SigH		 M. tuberculosis

110+1174

+1317+218

+368

 X 2.8 Hetero 6-mer ABCDEF:GH CDF GH 10331 5040 5291

aPDB ID: Four letter protein data bank ID;
bProtein: Name of the biomolecules;
cSource Organisms: Source of the sequence obtained from various organisms;
dProtein length: Length of the amino acid sequence;
eExperimental Methods: Biophysical methods used for the structure determination (X: X-ray, N:NMR);
fResolution (Å): Resolution of the macromolecules;
gOligomeric State: Total number of biomolecules in a biological assembly;
hPDB iChain Id: Chain Identifier from the PDB file;
jChain: Protein ,DNA and RNA chain involved in unique interface;
kBSA: buried surface area.