Table 2.
List of the 240 structures of protein-DNA complexes in the dataset.
| PDB code | DNA-binding subunits | Protein name | Species | Resolution /Å | DNA sequence |
| I. Helix-turn-helix group | |||||
| 1. Cro and Repressor family | |||||
| 1lmb* | 3,4 | Repressor | Phage λ | 1.8 | -AATACCACTGGCGGTGATATTATAT-CACCGCCAGTGGTAT- |
| 1lli | A,B | Repressor mutant | Phage λ | 2.1 | -AATACCACTGGCGGTGATATTATAT-CACCGCCAGTGGTAT- |
| 1per | L,R | Repressor | Phage 434 | 2.5 | AAGTACAGTTTTTCTTG-TATTATA--CAAGAAAAACTGTACT |
| 1rpe | L,R | Repressor | Phage 434 | 2.5 | -TATACAATGTATCTTG-TTTGACAAACAAGATACATTGTAT- |
| 2or1 | L,R | Repressor | Phage 434 | 2.5 | AAGTACAAACTTTCTTG-TATTATA--CAAGAAAGTTTGTACT |
| 3cro | L,R | Cro | Phage 434 | 2.5 | AAGTACAAACTTTCTTG-TATTATA--CAAGAAAGTTTGTACT |
| 6cro | A | Cro | Phage λ | 3.0 | AAGTACAAACTTTCTTG-TATTATA-CAAGAAAGTTTGTACT |
| 3orc | A | Cro | Phage λ | 3.0 | AAGTACAAACTTTCTTG-TATTATA--CAAGAAAGTTTGTACT |
| 2. Homeodomain family | |||||
| 1fjl*† | A,B,C,G | Paired protein | D. melanogaster | 2.0 | AATAATCTGATTACTGTAATCAGATTAT |
| 1hdd | C,D | Engrailed homeodomain | D. melanogaster | 2.8 | --TTTTGCCATGTAATTACCTAAATTAGGTAATTACATGGCAAA |
| 1apl | C,D | Mat α-2 | S. cerevisiae | 2.7 | --ACATGTAATTCATTTACACGCTGCGTGTAAATGAATTACATG |
| 1yrn | A,B | Mat a-1/α-2 | S. cerevisiae | 2.5 | -TACATGTAATTTATT-ACATCATATGATGTAATAAATTACATG |
| 1au7 | A1(5-76), | Pit-1 POU domain | R. norvegicus | 2.3 | TTGCGTAGCGTTACGTATATTCCGCTAATCGAT |
| A2(103-160), | |||||
| B1(5-75), | |||||
| B2(102-161) | |||||
| 1oct | C1(5-75) | Oct-1 POU domain | H. sapiens | 3.0 | TGTATTGCAAATAAGGACCTTATTTGCATAC |
| C1(102-161) | |||||
| 2hdd | A,B | Engrailed homeodomain | D. melanogaster | 1.9 | TGTTTTTGATAAGATCTTATCAAAAAC |
| 3hdd | A,B | Engrailed homeodomain | D. melanogaster | 2.2 | --TTTTGCCATGTAATTACCTAAATTAGGTAATTACATGGCAAA |
| 9ant | A,B | Antennapedia homeodomain | D. melanogaster | 2.4 | --TTTTGCCATGTAATTACCTAAATTAGGTAATTACATGGCAAA |
| 6pax | A | Paired domain | H. sapiens | 2.5 | GATGACCTAATAGGGAAAATAACACGAA |
| 1akh | A,B | Mat a-1/α-2 | S. cerevisiae | 2.5 | TACATGTAAAAATTACATCATATGA |
| 1b72 | A,B | Homeodomain | H. sapiens | 2.35 | ACTCTATGATTGATCGTAATGCGCAAACG |
| 1b8I | A,B | Homeodomain | D. melanogaster | 2.4 | TTTACGTTTAAAAGCTTAATAAACG |
| 1mnm | C,D | Mat α-2 | S. cerevisiae | 2.25 | GATTACCTAATAGGGAAATTTACACG |
| *** | |||||
| 3. LacI repressor family | |||||
| 1wet*† | A,C | Purine repressor | E. coli | 2.6 | AACGAAAACGTTTTCGT |
| 1bdh† | A,C | Purine repressor | E. coli | 2.7 | TACGCAAACGTTTGCGT |
| 1bdi† | A,C | Purine repressor | E. coli | 3.0 | TACGCAAACGTTTGCGT |
| 1pnr† | A,C | Purine repressor | E. coli | 2.7 | AACGAAAACGTTTTCG- |
| 2pua† | A,C | Purine repressor | E. coli | 2.9 | TACGCAAACGTTTGCGT |
| 2pub† | A,C | Purine repressor | E. coli | 2.7 | TACGCAAACGTTTGCGT |
| 2puc† | A,C | Purine repressor | E. coli | 2.6 | TACGCAAACGTTTGCGT |
| 2pud† | A,C | Purine repressor | E. coli | 2.6 | TACGCAAACGTTTGCGT |
| 2pue† | A,C | Purine repressor | E. coli | 2.7 | TACGCAAACGTTTGCGT |
| 2puf† | A,C | Purine repressor | E. coli | 3.0 | TACGCAAACGTTTGCGT |
| 2pug† | A,C | Purine repressor | E. coli | 2.7 | AACGAAAATTTTTCGT- |
| 1vpw† | A,C | Purine repressor | E. coli | 2.7 | TACGCAAACGTTTGCGT |
| 1qpz† | A,C | Purine repressor | E. coli | 2.5 | TACGCAAATTTTTCGT- |
| 1zay† | A,C | Purine repressor | E. coli | 2.7 | TACGCAAACGTTTGCGT |
| ********* | |||||
| 4. Endonuclease FokI family‡ | |||||
| 1fok* | A | Endonuclease FokI | F. okeanokoites | 2.8 | TCGGATGATAACGCTAGTCA |
| 5. γδ-resolvase family‡ | |||||
| 1gdt* | A,B | γδ-resolvase | E. coli | 3.0 | GCAGTGTCCGATAATTTATAAA |
| 6. Hin recombinase family‡ | |||||
| 1hcr* | A | Artificial Hin recombinase | Artificial | 1.8 | TGTTTTTGATAAGA |
| 7. RAP1 family | |||||
| 1ign* | A,B | RAP1 | S. cerevisiae | 2.25 | CCGCACACCCACACACCAG |
| 8. Prd paired domain family | |||||
| 1pdn* | C | Prd paired domain | D. melanogaster | 2.5 | AACGTCACGGTTGAC |
| 9. Tc3 transposase family‡ | |||||
| 1tc3* | C | Transposase TC3 | C. elegans | 2.45 | AGGGGGGGTCCTATAGAACTT |
| 10. Trp repressor family | |||||
| 1trr* | A,B,D,E, | Trp repressor | E. coli | 2.4 | AGCGTACTAGTACGCT |
| G,H,J,K | |||||
| 11. Diptheria Tox repressor family | |||||
| 1ddn* | A,B,C,D | Diptheria Tox repressor | E. coli | 3.0 | ATATAATTAGGATAGCTTTACCTAATTATTTTA |
| 12. Transcription factor IIB | |||||
| 1d3u* | B | TF IIB | P. woesei | 2.4 | AGAGTAAAGTTTAAATACTTATAT |
| 1vol | A | TF IIB | H. sapiens | 2.7 | ------ GGCTATAAAAGGGCTG-- |
| 1c9b | A,E,I,M,Q | TF IIB | H. sapiens | 2.65 | --GGGCGCCTATAAAAGGGG---- |
| ****** | |||||
| 'Winged' HTH | |||||
| 13. Interferon regulatory factor | |||||
| 2irf* | G,H,I,J, K, L | Interferon regulatory factor-2 | M. musculus | 2.2 | AAGTGAAAGCGA |
| 1if1 | A,B | Interferon regulatory factor | M. musculus | 3.0 | AACTGTAAGCTTT |
| 14. Catabolite gene activator protein family | |||||
| 2cgp* | C | Catabolite gene activator | E. coli | 2.2 | -------------------------GTCACATTAAT-------------------- |
| 1ber | A,B | Catabolite gene activator | E. coli | 2.5 | --------GCGAAAAGTGTGACATATGTCACACTTTTCGGCGAAAAGTGTGACATATGTCACACTT |
| 1cgp | A,B | Catabolite gene activator | E. coli | 3.0 | ACTTTTCGGCGAAAAGTGTGACATATGTCACACTTTTCGGCGAAAAGTGTGACATAT--------- |
| 1run | A,B | Catabolite gene activator | E. coli | 2.7 | --------GCGAAAAATGTGATCTAGATCACATTTTTCGGCGAAAAATGTGATCTAGATCACATTT |
| 1ruo | A,B | Catabolite gene activator | E. coli | 2.7 | --------GCGAAAAATGTGATCTAGATCACATTTTTCGGCGAAAAATGTGATCTAGATCACATTT |
| ************************************ | |||||
| 15. Transcription factor family | |||||
| 3hts*† | B | Heat shock transcription factor | K. lactis | 1.75 | GGTTCTAGAACC---- |
| 1cf7 | A,B | E2F-DP | H. sapiens | 2.6 | -ATTTTCGCGCGGTTT |
| ***** | |||||
| 16. Ets domain family | |||||
| 1bc8* | C | Sap-1 | H. sapiens | 1.93 | TACCGGAAGTAACTTCCGGT |
| 1bc7 | C | Sap-1 | H. sapiens | 2.01 | TACCGGAAGTAACTTCCGGT |
| 1pue | E,F | TF PU.1 | M. musculus | 2.1 | -AAAAAGGGGAAGTGGG--- |
| 1awc | A,B | GABP-α | M. musculus | 2.15 | -AACGACCGGAAGTACACCGGA |
| ***** | |||||
| II. Zinc-coordinating group | |||||
| 17. ββα-zinc finger family | |||||
| 1aay* | A1(103-133), A2(134-161), A3(162-187) | Zif268 zinc finger | M. musculus | 1.6 | --AGCGTGGGCGTTACGCC-CACGC |
| 1zaa | C1(3-33), C2(34-61), C3(62-87) | Zif268 zinc finger | M. musculus | 2.1 | --AGCGTGGGCGTTACGCC-CACGC------------- |
| 2drp | A1(103-135), A2(137-164), D1(102-135), D2(137-165) | Tramtrack protein | D. melanogaster | 2.8 | AATAAGGATAACGTCCGTCGGACGTTATCCTTATTA-- |
| 1ubd | C1(295-323), C2(324-351), C3(352-381), C4(382-408) | Zinc finger | H. sapiens | 2.5 | -AGGGTCTCCAATTTTGAAGCGCGCTTCAAAATGG--- |
| 1mey | C1(1-31), C2(32-59), C3(60-84), F1(1-31), F2(32-59), F3(60-84), G | Consensus zinc finger | Artificial | 2.2 | ---ATGAGGCAGAACTTAGTTCTGCCTCA-------- |
| 1a1g | A1(103-132), A2(133-159), A3(160186) | DSNR (Zif268 variant) | M. musculus | 1.9 | ---AGCGTGGGCGTTACGCCCACGC |
| 1a1h | " | QSGR (Zif268 variant) | M. musculus | 1.6 | ---AGCGTGGGCGTTACGCCCACGC |
| 1a1I | " | RADR (Zif268 variant) | M. musculus | 1.9 | ---AGCGTGGGCGTTACGCCCACGC |
| 1a1j | " | " | M. musculus | 1.6 | ---AGCGTGGGCGTTACGCCCACGC |
| 1a1k | " | " | M. musculus | 2.0 | ---AGCGTGGGCGTTACGCCCACGC |
| 1a1l | " | Zif268 zinc finger | M. musculus | 2.3 | ---AGCGTGGGCGTTACGCCCACGC |
| 2gli | A1(103-135) | Five-zinc finger | H. sapiens | 2.6 | ---AGCGTGGGCGTTACGCCCACGC |
| A2(136-167) | " | " | " | ---TTTCGTCTTGGGTGGTCCACG | |
| A3(168-196) | " | " | " | ||
| A4(197-228) | " | " | " | ||
| A5(229-257) | " | " | " | ||
| 18. Hormone-nuclear receptor family | |||||
| 2nll* | A,B | Retinoic acid receptor | H. sapiens | 1.9 | ---CAGGTCAT-TTCAGGTCAGCTGACCTGAAATGACCTG-- |
| 1hcq | A,B,E,F | Estrogen receptor | H. sapiens | 2.4 | --CCAGGTCAC-AGTGACCTGCCAGGTCACTG-TGACCTG-- |
| 1glu | A,B | Glucococorticoid receptor | R. norvegicus | 2.9 | --CCAGAACATCGATGTTCTGCCAGAACATCGATGTTCTG-- |
| 1lat | A,B | Glucococorticoid receptor | R. norvegicus | 1.9 | TTCCAGAACATGTTCTGGATTCCAGAACAT----GTTCTGGA |
| 1by4 | A,B,C,D | Retinoic acid receptor | H. sapiens | 2.1 | ---CAGGACATCTAGTAAATTCCAGATCTTACGTTGTCTG-- |
| 1cit | A | Orphan nuclear receptor | H. sapiens | 2.7 | --CCAGAACATCGAGCCTCTGCCAGAACATCGTTGTTCTG-- |
| 1a6y | A,B | Orphan nuclear receptor | H. sapiens | 2.3 | -TCCAGGACATCGCTAAGCTTGCTGGTCATTGCGGTTCTG |
| *********** | |||||
| 19. Loop-sheet-helix family | |||||
| 1tsr* | A,B,C | p53 tumor suppressor | H. sapiens | 2.2 | TTTCCTAGACTTGCCCAATTAATAATTGGGCAAGTCTAGGAA |
| 1tup | A,B,C | p53 tumor suppressor | H. sapiens | 2.2 | TTTCCTAGACTTGCCCAATTAATAATTGGGCAAGTCTAGGAA |
| 20. GAL4-type family: | |||||
| 1zme* | C,D | Proline utilization | S. cerevisiae | 2.5 | -ACGGGAAGCCAACTCCG- |
| 1d66 | A,B | GAL4 | S. cerevisiae | 2.7 | CCGGAGGACAGTCCTCCGG |
| ******** | |||||
| III. Zipper-type group | |||||
| 21. Leucine zipper family | |||||
| 2dgc*† | A,C | GCN4 | S. cerevisiae | 2.2 | ---TGGAGATGACGTCATCTCC-- |
| 1dgc† | A,C | GCN4 | S. cerevisiae | 3.0 | ---TGGAGATGACGTCATCTCC-- |
| 1ysa | C,D | GCN4 | S. cerevisiae | 2.9 | ---TTCCTATGAGCTCATCCAGTT |
| 1a02 | F | C-Fos | H. sapiens | 2.7 | TTGGGAAATTTCTTTCATAG---- |
| J | C-Jun | ||||
| ***** | |||||
| 22. Helix-loop-helix family | |||||
| 1am9* | A,B,C,D | Srebp-1A | H. sapiens | 2.3 | -TTGCAAGTGGGGTGATCCATGA--------------- |
| 1hlo | A,B | Max | H. sapiens | 2.8 | -CACCACGTGGTGTGGTGCACCA--------------- |
| 1an4 | A,B | USF | H. sapiens | 2.9 | AGGCCACGTGACCGG-GGTACATCCGGTGCACT----- |
| 1an2 | A,C | Max | M. musculus | 2.9 | AGGTCACGTGACCTACACCACATCCAGTGCACTGGATG |
| 1mdy | A,B,C,D | Myod | M. musculus | 3.0 | TCAACAGCTGTTGA---TCAACAGCTGTTGAC------ |
| 1a0a | A,B | Pho4 | S. cerevisiae | 2.8 | |
| ********* | |||||
| IV. Other α-helix group | |||||
| 23. Papillomavirus-1 E2 family | |||||
| 2bop*† | A,C | Papillomavirus-1 E2 | Bovine | 1.7 | CCGACCGACGTCGGTCG |
| papillomavirus | |||||
| 24. Histone family | |||||
| 1aoi* | A,B,C,D,E,F,G,H | Histone | X. laevis | 2.8 | ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTC |
| CATCAAAAGGCATGTTCAGCTGAATTCAGCTGAACATGCCTTTTGATGG | |||||
| AGCAGTTTCCAAATACACTTTTGGTAGAATCTGCAGGTGGATATTGAT | |||||
| 25. EBNA1 nuclear protein family | |||||
| 1b3t* | A,B | Ebna-1 | H. herpesvirus 4 | 2.2 | GGGAAGCATAGCTTCCC |
| 26. Skn-1 transcription factor | |||||
| 1skn* | P | Skn-1 | C. elegans | 2.5 | TGACAATGTCATCCC |
| 27. Cre recombinase family‡ | |||||
| 1crx* | A,B | Cre recombinase | Bacteriophage P1 | 2.4 | TATAACTTCGTATAG |
| 28. High mobility group family | |||||
| 1qrv* | A,B | High mobility group-1 | D. melanogaster | 2.2 | GCGATATCGC------ |
| 1ckt | A | High mobility group-1 | R. norvegicus | 2.5 | CCCCTCTGGACCTTCC |
| ** | |||||
| 29. MADS box family | |||||
| 1mnm* | A,B | Pheromone transcription | S. cerevisiae | 2.25 | GATTACCTAATAGGGAAATTTACACG |
| factor MCM-1 | |||||
| V. β-sheet group | |||||
| 30. TATA box-binding family | |||||
| 1ytb* | B | TATA box-binding protein | S. cerevisiae | 1.8 | --GTATATAAAACGGGTGGCGTTTTATATAC----- |
| 1ytf | A | TATA box-binding protein | S. cerevisiae | 2.5 | ----TGTATGTATATAAAACGTTTTATATACATACA |
| 1ais | A | TATA box-binding protein | P. woesei | 2.1 | AACTTACTTTIIAAAGCTTGAATGAAAAATTTCA-- |
| 1cdw | A | TATA box-binding protein | H. sapiens | 1.9 | CTGCTATAAAAGGCTGCAGCCTTTTATAGCAG---- |
| 1tgh | A | TATA box-binding protein | H. sapiens | 2.0 | --------CGTATATATACGCGTATATATACG---- |
| 1vol | B | TATA-box-BP | H. sapiens | 2.7 | ----TGATCCCTTAAACTCGCTTGTATATGA----- |
| 1d3u | A | TATA-box-BP | P. woesei | 2.4 | ---CTTAATCGCTATATCCGTTTCTATAGCTTTCA- |
| 1c9b | B,F,J,N,R | TATA-box-BP | H. sapiens | 2.65 | --GCTATAACGGTTAACGTTATTGTATAGCCAA--- |
| ***** | |||||
| VI. β-hairpin/ribbon group | |||||
| 31. MetJ repressor protein | |||||
| 1cma* | A,B | Met repressor | E. coli | 2.8 | TTAGACGTCTAGACGTCTA |
| 32. Tus replication terminator family | |||||
| 1ecr* | A | Tus replication terminator | E. coli | 2.7 | TTAGTTACAACATACT |
| 33. Integration host factor family | |||||
| 1ihf* | A,B | Integration host factor | E. coli | 2.5 | CGGTGCAACAAATTGATAAGCAATGCTTTTTTGGC |
| 34. Transcription factor T-domain | |||||
| 1xbr* | A,B | T-domain | X. laevis | 2.5 | AATTTCACACCTAGGTGTGAAAATT |
| 35. Hyperthermophile DNA-BP. | |||||
| 1azp* | A | Sac7D | S. acidocaldarius | 1.6 | GCGATCGC |
| 1azq | A | Sac7D | S. acidocaldarius | 1.94 | GCGATCGC |
| 1bnz | A | 7A | S. acidocaldarius | 2.0 | GTAATTAC |
| 1bf4 | A | Ss07D | S. acidocaldarius | 1.6 | GTAATTAC |
| **** | |||||
| 36. Arc repressor | |||||
| 1bdt* | A,B,C,D | Arc repressor | Bacteriophage P22 | 2.5 | TATAGTAGAGTGCTTCTATCAT |
| 1bdv | A,B,C,D | Arc repressor | Bacteriophage P22 | 2.8 | TATAGTAGAGTGCTTCTATCAT |
| 1par | A,B,C,D | Arc repressor | Bacteriophage P22 | 2.6 | TATAGTAGAGTGCTTCTATCAT |
| VII. Other | |||||
| 37. Rel homology region family | |||||
| 1a3q* | A, B | NF κB p52 | H. sapiens | 2.1 | GATTCCCCGGGGAATTCCCC------ |
| 1nfk | A,B | NF-κB p50 | M. musculus | 2.3 | GAATTCCCTGGGAATTCCC------- |
| 1svc | P,T | NF-κB p50 | H. sapiens | 2.6 | ----AGATGGGGAATCCCCTAGA--- |
| 1vkx | A,B | NF κB p50/p65 | M. musculus | 2.9 | ------CTGGGGAATTTCCCAG---- |
| 1ram | A,B | NF κB p65 | M. musculus | 2.7 | GGGACTTTCCGAAATTCCCC------ |
| 1bvo | A | Gambif1 TF | A. gambiae | 2.7 | ---CGGGCTGGAAATTTCCAGCCG-- |
| 1a02 | N | Nfat | H. sapiens | 2.7 | ------TTGGGAAATTTCTTTCATAG |
| ***** | |||||
| 38. Stat protein family | |||||
| 1bf5* | A | Stat-1 | H. sapiens | 2.9 | ACAGTTTCCCGTAAATGC |
| VIII. Enzyme group | |||||
| 39. Methyltransferase family | |||||
| 6mht* | A | Hhal methyltransferase | H. haemolyticus | 2.05 | ---GATAGCGCTATCTGATAGCGCTATC---------- |
| 4mht | A | Hhal methyltransferase | H. haemolyticus | 2.7 | ---GATAG-GCTATC-GATAGCGCTATC---------- |
| 1mht | A | Hhal methyltransferase | H. haemolyticus | 2.8 | ---GATAGCGCTATCTGATAGCGCTATC---------- |
| 3mht | A | Hhal methyltransferase | H. haemolyticus | 2.7 | ---GATAGCGCTATCTGATAGCGCTATC---------- |
| 5mht | A | HhaI methyltransferase | H. haemolyticus | 2.7 | ---GATAGCGCTATCTGATAGCGCTATC---------- |
| 7mht | A | HhaI methyltransferase | H. haemolyticus | 2.87 | ---GATAGCGCTATCTGATAGCGCTATC---------- |
| 8mht | A | HhaI methyltransferase | H. haemolyticus | 2.76 | ---GATAGCGCTATCTGATAGCGCTATC---------- |
| 9mht | A | HhaI methyltransferase | H. haemolyticus | 2.87 | ---GATAG-GCTATC-GATAGCGCTATC---------- |
| 10mh | A | HhaI methyltransferase | H. haemolyticus | 2.55 | ---GATAGCGCTATCTGATAGCGCTATC---------- |
| 1dct | A,B | HaeIII methyltransferase | H. aegyptus | 2.8 | ---ACCAGCAG-GCCACC-AGTGTCACTGGTGGCCTGCTGG |
| ********** | |||||
| 40. Endonuclease PvuII family | |||||
| 3pvi* | A,B | Endonuclease PvuII | P. vulgaris | 1.59 | TGACCAGCTGGTC |
| 2pvi | A,B | Endonuclease PvuII | P. vulgaris | 1.76 | TGACCAGCTGGTC |
| 1pvi | A,B | Endonuclease PvuII | P. vulgaris | 2.8 | TGACCAGCTGGTC |
| 41. Endonuclease EcoRV family | |||||
| 1rva* | A,B | Endonuclease EcoRV | E. coli | 2.0 | ------AAAGATATCTTAAA---GATATCTT- |
| 1rvb | A,B | Endonuclease EcoRV | E. coli | 2.1 | ------AAAGATATCTTAAA---GATATCTT- |
| 1rvc | A,B | Endonuclease EcoRV | E. coli | 2.1 | ------AAAGATATCTTAAA---GATATCTT- |
| 2rve | A,B | Endonuclease EcoRV | E. coli | 3.0 | CGAGCTCGCGAGCTCGCGAGCTCGCGAGCTCG |
| 4rve† | A,B,C,G | Endonuclease EcoRV | E. coli | 3.0 | -------GGGATATCCCGG----GATATCCC- |
| 1rve | A,B | Endonuclease EcoRV | E. coli | 2.5 | ------AAAGATATCTTAAA----GATATCTT- |
| 1rv5 | A,B | Endonuclease EcoRV | E. coli | 2.1 | ------CGGGATATCCC CGG---GATATCCC- |
| 1bgb | A,B | Endonuclease EcoRV | E. coli | 2.0 | ------AAAGATATCTTAAA---GATATCTT- |
| 1bss | A,B | Endonuclease EcoRV | E. coli | 2.0 | ------AAAGATATCTTAAA---GATATCTT- |
| 1bua | A,B | Endonuclease EcoRV | E. coli | 2.15 | ------AAAGACATCTT--------------- |
| 1bsu | A,B | Endonuclease EcoRV | E. coli | 2.0 | ------AAAGACATCTT--------------- |
| ******* | |||||
| 42. Endonuclease EcoRI family | |||||
| 1qps*† | A,M | Endonuclease EcoRI | E. coli | 2.5 | TCGCGAATTCGCG |
| 1eri† | A,C | Endonuclease EcoRI | E. coli | 2.7 | TCGCGAATTCGCG |
| 1qrh† | A | Endonuclease EcoRI | E. coli | 2.5 | TCGCGAATTCGCG |
| 1qri† | A | Endonuclease EcoRI | E. coli | 2.6 | TCGCGAATTCGCG |
| 43. Endonuclease BamHI family | |||||
| 3bam* | A,B | Endonuclease BamHI | B. amyloliquefaciens | 1.8 | TATGGATCCATATATG |
| 1bhm | A,B | Endonuclease BamHI | B. amyloliquefaciens | 2.2 | TATGGATCCATA---- |
| ************ | |||||
| 44. Endonuclease V family | |||||
| 1vas* | A | Endonuclease V | Phage T4 | 2.75 | ATCGCGTTGCGCTTAGCGCAACGCCGA |
| 45. Dnase I family | |||||
| 2dnj* | A | Deoxyribonuclease I | B. taurus | 2.0 | GCGATCGCGCGATC-- |
| 1dnk | A | Deoxyribonuclease I | B. taurus | 2.3 | GGTATACGGCTATACC |
| ****** | |||||
| 46. DNA mismatch endonuclease | |||||
| 1cw0* | A | DNA mismatch endonuclease | E. coli | 2.3 | ACGTACCTGGCTAGCTAGGTACGT |
| 47. DNA polymerase-β family | |||||
| 1bpy* | A | DNA polymerase-β | H. sapiens | 2.2 | CCGACCACGCATCAGC |
| 1bpx | A | " | " | 2.4 | CCGACCACGCATCAGC |
| 1bpz | A | " | " | 2.6 | CCGACCACGCATCAGC |
| 1zqa | A | " | " | 2.7 | CATTAGAATCTAATG- |
| 1zqf | A | " | " | 2.9 | CATTAGAATCTAATG- |
| 1zqi | A | " | " | 2.7 | CATTAGAATCTAATG- |
| 1zqn | A | " | " | 3.0 | CATTAGAATCTAATG- |
| 1zqp | A | " | " | 2.8 | CATCTG--TCAGATG- |
| 7ice | A | " | " | 2.8 | CATCTG--TCAGATG- |
| 7icg | A | " | " | 3.0 | CATCTG--TCAGATG- |
| 7ich | A | " | " | 2.9 | CATCTG--TCAGATG- |
| 7ici | A | " | " | 2.8 | CATCTG--TCAGATG- |
| 7ick | A | " | " | 2.9 | CATCTG--TCAGATG- |
| 7icm | A | " | " | 3.0 | CATCTG--TCAGATG- |
| 7icn | A | " | " | 2.8 | CATCTG--TCAGATG- |
| 7icp | A | " | " | 3.0 | CATCTG--TCAGATG- |
| 7icq | A | " | " | 2.9 | CATCTG--TCAGATG- |
| 7icr | A | " | " | 3.0 | CATCTG--TCAGATG- |
| 7ics | A | " | " | 2.8 | CATCTG--TCAGATG- |
| 7ict | A | " | " | 2.8 | CATCTG--TCAGATG- |
| 7icv | A | " | " | 2.8 | CATCTG---CAGATG- |
| 8ica | A | " | " | 3.0 | CATTAGAATCTAATG- |
| 8icc | A | " | " | 2.8 | CATTAGAATCTAATGA |
| 8icf | A | " | " | 2.9 | CATTAGAATCTAATG- |
| 8ici | A | " | " | 2.8 | CATTAGAATCTAATGA |
| 8ick | A | " | " | 2.7 | CATTAGAATCTAATG- |
| 8icm | A | " | " | 2.9 | CATTAGAATCTAATGA |
| 8icn | A | " | " | 2.8 | CATTAGAATCTAATG- |
| 8ico | A | " | " | 2.7 | CATTAGAATCTAATGA |
| 8icp | A | " | " | 2.9 | CATTAGAATCTAATG- |
| 8icq | A | " | " | 3.0 | CATTAGAATCTAATGA |
| 8icr | A | " | " | 2.9 | CATTAGAATCTAATGA |
| 8ics | A | " | " | 2.9 | CATTAGAATCTAATGA |
| 8icu | A | " | " | 3.0 | CATTAGAATCTAATG- |
| 8icx | A | " | " | 3.0 | CATTAGAATCTAATG- |
| 9ica | A | " | " | 3.0 | CATTAGAA-CTAATG- |
| 9icf | A | " | " | 3.0 | CATTAGAT-CTAATG- |
| 9icg | A | " | " | 3.0 | CATTAGAT-CTAATG- |
| 9ich | A | " | " | 2.9 | CATTAGAT-CTAATG- |
| 9ick | A | " | " | 2.7 | CATTAGAT-CTAATG- |
| 9icl | A | " | " | 2.8 | CATTAGAT-CTAATG- |
| 9icm | A | " | " | 2.9 | CATTAGAT-CTAATG- |
| 9icn | A | " | " | 3.0 | CATTAGAATCTAATG- |
| 9ico | A | " | " | 2.9 | CATTAGAATCTAATG- |
| 9icq | A | " | " | 2.9 | CATTAGAATCTAATG- |
| 9icr | A | " | " | 3.0 | CATTAGAA-CTAATG- |
| 9ics | A | " | " | 2.9 | CATTAGAT-CTAATG- |
| 9ict | A | " | " | 3.0 | CATTAGAT-CTAATG- |
| 9icu | A | " | " | 2.9 | CATTAGAATCTAATG- |
| 9icv | A | " | " | 2.7 | CATTAGAATCTAATG- |
| 9icw | A | " | " | 2.6 | CATTAGAATCTAATG- |
| 9icx | A | " | " | 2.6 | CATTAGAATCTAATG- |
| 9icy | A | " | " | 3.0 | CATTAGAATCTAATG- |
| 2bpf | A | " | R. norvegicus | 2.9 | GGGCGCCGCGGCGCC- |
| *** | |||||
| 48. DNA polymerase I | |||||
| 2bdp* | A | DNA polymerase I | B. stearothermophilus | 1.8 | --GCATGATGCAGCATCATGC--- |
| 4bdp | A | DNA polymerase I | B. stearothermophilus | 1.8 | --GCATGATGCAGCATCATGC--- |
| 1qsy | A | DNA polymerase I | T. aquaticus | 2.3 | GACCACGGCGCAGGGCGCCGTGGT |
| 1qss | A | DNA polymerase I | T. aquaticus | 2.3 | GACCACGGCGCAGGGCGCCGTGGT |
| 2ktq | A | DNA polymerase I | T. aquaticus | 2.3 | GACCACGGCGCGGGCGCCGTAATC |
| 3ktq | A | DNA polymerase I | T. aquaticus | 2.3 | GACCACGGCGCGGGCGCCGTAATC |
| 4ktq | A | DNA polymerase I | T. aquaticus | 2.5 | GACCACGGCGCGGGCGCCGTAATC |
| 1tau | A | DNA polymerase I | T. aquaticus | 3.0 | -GCCATGCGGCAGTCGC------- |
| 1d8y | A | DNA polymerase I | E. coli | 2.08 | TTTTTTTTTTTTTTTTT |
| ****** | |||||
| 49. DNA polymerase T7 | |||||
| 1t7p* | A | DNA polymerase | Bacteriophage | 2.2 | GCCAGTGCCAACCTTGGCACTGGC |
| 1clq | A | DNA polymerase | Bacteriophage | 2.7 | GCGGAACTACTAGTAGTTCCGAG |
| ****** | |||||
| 50. HIV reverse transcriptase | |||||
| 1hmi* | A,B | HIV reverse transcriptase | HIV type 1 | 2.8 | ATGGCGCCCGAACAGGAC |
| 2hmi | A,B | HIV reverse transcriptase | HIV type 1 | 2.8 | ATGGCGCCCGAACAGGAC |
| 51. Uracil-DNA glycosylase | |||||
| 1ssp* | E | Uracil-DNA glycosylase | H. sapiens | 1.9 | CTGTATCTTAAAGATAACAG |
| 2ssp | E | Uracil-DNA glycosylase | H. sapiens | 2.25 | CTGTATCTTAAAGATAACAG |
| 4skn | A | Uracil-DNA glycosylase | H. sapiens | 2.9 | TGGGGGCTTAAAGCCGCCC- |
| ********* | |||||
| 52. 3-Methyladenine DNA glycosylase | |||||
| 1bnk* | A | 3-Methyladenine DNA glycosylase H. | H. sapiens | 2.7 | GACATGTTGCCTGGCAATCATGTCA |
| 53. Homing endonuclease | |||||
| 1a73* | A,B, | Intron-encoded | P. polycephalum | 1.8 | -TTGACTCTCTTAAGCGAGTCA |
| Endonuclease I-Ppoi | |||||
| 1a74 | A,B, | Intron-encoded | P. polycephalum | 2.2 | -TTGACTCTCTTAAGCGAGTCA |
| Endonuclease I-Ppoi | |||||
| 1cyq | A,B, | Intron-encoded | P. polycephalum | 1.93 | -TTGACTCTCTTAAGCGAGTCA |
| Endonuclease I-Ppoi | |||||
| 1ipp | A,B, | Intron-encoded | P. polycephalum | 2.2 | -TTGACTCTCTTAAGCGAGTCA |
| Endonuclease I-Ppoi | |||||
| 1bp7 | A,B,C,D | Homing endlonuclease | C. reinhardtii | 3.0 | GCAAAACGTCGTGAGACAGTTCG |
| I-CreI | |||||
| ********* | |||||
| 54. Topoisomerase I | |||||
| 1a31* | A | Topoisomerase I | H. sapiens | 2.1 | AAAAAGACCCTGAAAAACCCCT |
| 1a35 | A | Topoisomerase I | H. sapiens | 2.5 | AAAAAGACCCTGAAAAACCCCT |
| 1a36 | A | Topoisomerase I | H. sapiens | 2.8 | AAAAAGACTTAGAAAAATTTTT |
Each entry is provided with the four-digit PDB code, the name, the source, resolution and the aligned sequences of DNA to which the protein is bound in the crystal structure. Protein DNA-binding domains are identified by a single letter identifying the protein chain in the PDB file. Where more than one DNA-binding domain is contained in a single subunit, the chain is split into the individual domains. For these, the domains are labeled with the chain ID and a number and the PDB file residue numbers of the domain are given in brackets. The PDB entries are classified into 'groups' and 'families' according to the structure of the protein contained in the complex. The representative for each family, defined as the structure with the highest resolution is marked with an asterisk (*). The CAP family is an exception; the highest-resolution entry, 2cgp, contains only part of the dimer and so PDB code 1ber is used as the representative. The full coordinate files for homodimeric PDB entries that contain only half the structure were obtained from the NDB and are marked by a dagger (†). Enzyme families whose structures also qualified for another protein group are listed in all that are applicable and are marked by a double dagger (‡).