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PDB ID Mentions in PubMed Central Article count: 5

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PDB ID Mentions in PubMed Central

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DNA-binding residues and binding mode prediction with binding-mechanism concerned models.

(2009) BMC Genomics 10 Suppl 3

PubMed: 19958487 | PubMedCentral: PMC2788376 | DOI: 10.1186/1471-2164-10-S3-S23

Table 5 Dataset of 253 TF-DNA complexes for DNA-binding residues prediction 253 TF-DNA Complexes 1A02:F 1A02:J 1A0A:A 1A0A:B 1A6Y:A 1A6Y:B 1AKH:A 1AKH:B 1AM9:A 1AM9:B 1AM9:C 1AM9:D 1AN2:A 1AN4:A 1AN4:... 1APL:C 1APL:D 1AU7:A 1AU7:B 1B01:A 1B01:B 1B72:B 1B8I:B 1BDT:A 1BDT:B 1BDT:C 1BDT:D 1BDV:A 1BDV:B 1BDV:C 1BDV:D 1BY4:A 1BY4:B 1BY4:C 1BY4:D 1C0W:A 1C0W:B 1C0W:C 1C0W:D 1CF7:A 1CF7:B 1CGP:A 1CGP:B 1CMA:A 1CMA:B 1CQT:A 1D5Y:A 1D5Y:B 1D5Y:C 1D5Y:D 1D66:A 1D66:B 1DDN:A 1DDN:B 1DDN:C 1DDN:D 1DSZ:A 1DSZ:B 1DU0:A 1DU0:B 1EA4:A 1EA4:B 1EA4:D 1EA4:E 1EA4:F 1EA4:G 1EA4:H 1EA4:J 1EA4:K 1EA4:L 1F2I:G 1F2I:H 1F2I:I 1F2I:J 1F2I:K 1F2I:L 1F5T:A 1F5T:B 1F5T:C 1F5T:D 1FJL:A 1FJL:B 1FJL:C 1FOS:E 1FOS:F 1FOS:G 1FOS:H 1G2D:C 1G2D:F 1G2F:C 1G2F:F 1GDT:A 1GDT:B 1H88:A 1H88:B 1H89:A 1H89:B 1H8A:A 1H8A:B 1H9T:A 1H9T:B 1HCQ:A 1HCQ:B 1HDD:C 1HDD:D 1HF0:A 1HF0:B 1HJB:A 1HJB:B 1HJB:D 1HJB:E 1HLO:A 1HLO:B 1HW2:A 1HW2:B 1HWT:C 1HWT:D 1HWT:G 1HWT:H 1IO4:A 1IO4:B 1JGG:A 1JGG:B 1JNM:A 1JNM:B 1JT0:A 1JT0:B 1JT0:C 1JT0:D 1JWL:A 1JWL:B 1K61:A 1K61:B 1K61:C 1K61:D 1KB2:A 1KB2:B 1KB4:A 1KB4:B 1KB6:A 1KB6:B 1KU7:A 1L3L:A 1L3L:B 1L3L:C 1L3L:D 1LAT:A 1LAT:B 1LB2:A 1LE8:A 1LE8:B 1LLI:A 1LLI:B 1LLM:C 1LMB:3 1LMB:4 1MDY:A 1MDY:C 1MDY:D 1MEY:C 1MEY:F 1MJM:A 1MJM:B 1MJP:A 1MJP:B 1MNM:C 1MNM:D 1NKP:A 1NKP:B 1NKP:D 1NKP:E 1NLW:A 1NLW:B 1NLW:D 1NLW:E 1P47:A 1P47:B 1PAR:A 1PAR:B 1PAR:C 1PAR:D 1PER:L 1PER:R 1PUF:A 1PUF:B 1PYI:A 1PYI:B 1QP9:A 1QP9:B 1QP9:C 1QP9:D 1R0N:A 1RPE:L 1RPE:R 1TF6:A 1TF6:D 1TRO:A 1TRO:C 1TRO:E 1TRO:G 1TRR:A 1TRR:B 1TRR:D 1TRR:E 1TRR:G 1TRR:H 1TRR:J 1TRR:K 1YRN:A 1YRN:B 1YSA:C 1YSA:D 1ZME:C 1ZME:D 2DRP:A 2DRP:D 2HAP:C 2HAP:D 2HDD:A 2HDD:B 2NLL:A 2NLL:B 2OR1:L 2OR1:R 2PRT:A 2QL2:A 2QL2:B 2QL2:C 2QL2:D 2R5Y:A 2R5Y:B 3BPY:A 3CBB:A 3CBB:B 3CO6:C 3COQ:A 3COQ:B 3D0A:A 3D0A:B 3D0A:C 3D0A:D 3DFX:A 3DFX:B 3DZY:A 3DZY:D 3E00:A 3E00:D 3EXJ:A 3EXJ:B 3EXL:A 3HDD:A 3HDD:B 9ANT:A Defining the DNA-binding residue Previous research used various distance cut-offs from 3.5 Å to 6 Å to define DNA-binding residues between proteins and DNA [ 6 - 10 , 14 , 40 , 42 ].

Publication Year: 2009


Benchmarks for flexible and rigid transcription factor-DNA docking.

(2011) BMC Struct Biol 11

PubMed: 22044637 | PubMedCentral: PMC3262759 | DOI: 10.1186/1472-6807-11-45

(Å) SCOP Protein Oligo_state DNA CopG repressor 1b01 2.56 a.43.1.3 A, B Homodimer E, F 5 2cpg 1.60 A, B 0.511 0.460 PhoB 1gxp a 2.50 a.4.6.1 A Monomer C, D 7 1gxq 2.00 A 1.622 1.622 AML1 Runt ... omain 1hjc 2.65 b.2.5.6 D Monomer E, F 6 1ean 1.70 A 1.056 1.056 Papillomavirus E2 1jj4 2.40 d.58.8.1 A, B Heterodimer C, D 10 1f9f 1.90 C, D 0.949 1.484 TATA-binding protein 1qn4 1.86 d.129.1.1 B Monomer E, F 15 1vok 2.10 B 0.934 0.934 Tet repressor 1qpi 2.50 a.4.1.9 A, C Homodimer B, M 14 2tct 2.10 A, B 2.061 1.359 MtaN 1r8d 2.70 a.6.1.3 A, B Homodimer C, D 8 1jbg 2.75 A, B 2.107 1.368 Sigma subunit domain 4 1rio a 2.30 a.4.13.2 H Monomer U, T 6 1ku3 1.80 A 1.405 1.405 Easy MecI 1sax 2.80 a.4.5.39 A, B Homodimer C, D 12 1okr 2.40 A, B 1.718 1.586 CAP 2cgp 2.20 a.4.5.4 A, F Homodimer B, C, D, E 10 1i5z 1.90 A, B 1.652 1.919 LRP/ASNC family protein 2e1c 2.10 a.4.5.32 A, F Homodimer B, D 12 2zny 2.59 A, B 1.339 1.184 IdeR 2it0 a 2.60 a.4.5.24 C, D Homodimer E, F 11 2isy 1.96 A, B 0.476 0.489 Phi 434 repressor 2or1 2.50 a.35.1.2 R, L Homodimer A, B 17 1r69 c 2.00 A, B 0.570 0.493 PutA 2rbf 2.25 N/A A, B Homodimer C, D 8 2gpe 1.90 A, B 0.798 0.571 SoxR 2zhg 2.80 a.6.1.3 A, D Homodimer B, C 6 2zhh 3.20 A, B 1.749 1.467 Controller protein 3clc a 2.80 a.35.1.3 C, D Homodimer E, F 14 3fya 3.00 A, B 0.834 0.809 CprK 3e6c 1.80 a.4.5.4 C, D Homodimer A, B, E, F 12 3e5u 1.83 A, B 1.060 0.906 NrtR 3gz6 2.90 N/A A, B Homodimer C, D 15 3gz5 2.20 A, B 0.853 0.726 Max 1an2 2.90 a.38.1.1 A, C Homodimer B, D 10 1r05 d N/A A, B 8.074 4.767 RXR-alpha 1by4 2.10 g.39.1.2 A, B Homodimer E, F 8 1rxr c, d N/A A, B 4.637 2.326 Met repressor 1cma 2.80 a.43.1.5 A, B Homodimer C, D 4 1cmc 1.80 A, B 2.232 2.313 Myb 1h8a a 2.23 a.4.1.3 C Monomer D, E 8 1gv2 1.68 A 9.153 9.153 QacR 1jt0 a 2.90 a.4.1.9 B, D Homodimer E, F 12 1jt6 2.54 D, E 2.924 1.650 Lambda repressor 1lmb 1.80 a.35.1.2 3, 4 Homodimer 1, 2 10 1lrp 3.20 A, B 32.342 0.928 Trp repressor 1tro a 1.90 a.4.12.1 A, C Homodimer I, J 12 1p6z 1.67 N, R 3.095 1.427 Prospero 1xpx 2.80 a.4.1.1 A Monomer C, D 3 1mij 2.05 A 0.519 0.519 Hard OhrR 1z9c 2.64 a.4.5.28 C, D Homodimer I, J 12 1z91 2.50 A, B 2.521 1.919 Put3 1zme 2.50 g.38.1.1 C, D Homodimer A, B 5 1ajy d N/A A, B 9.326 8.725 Phi lambda phage cII 1zs4 1.70 a.35.1.9 A, B, C, D HT f U, T 14 1zpq 2.80 A, B, C, D 4.947 2.679 p53 2ac0 1.80 b.2.5.2 A, B, C, D HT f E, F, G, H 21 2j1y 1.69 A, B, C, D 25.325 0.932 Omega repressor 2bnw 2.45 a.43.1.4 A, B Homodimer E, F 4 1irq 3.50 A, B 0.887 1.049 ILF 2c6y 2.40 a.4.5.14 A Monomer C, D 8 1jxs d N/A A 2.830 2.830 Phi 29 protein p4 2fio 2.70 N/A A, B Homodimer C, D 4 2fip 2.00 C, D 0.679 0.496 IRF-2 2irf a 2.20 a.4.5.23 L Monomer C, D 6 1irf d N/A A 3.459 3.459 CgmR 2yvh a 2.50 N/A C, D Homodimer E, F, G, H 10 2yve 1.40 A, B 2.663 1.599 HipB 3dnv 2.68 N/A B, C Homodimer E, T 10 2wiu 2.35 B, D 3.511 2.925 Engrailed homeodomain 3hdd a 2.20 a.4.1.1 A Monomer C, D 4 1enh 2.10 A 0.716 0.716 a Has more than one binding unit b NRBC: number of protein residues having side-chain contacts with DNA bases c Modeled unit structure d NMR structure, resolution N/A e RMSD u : global RMSD between bound and unbound TF-units, RMSD c : global RMSD between bound and unbound TF-chains f HT: homotetramer Table 2 Rigid TF-DNA docking benchmark TF-DNA Complex Name PDB TF-DNA Unit Chains ID Res.

(Å) SCOP Protein Oligo_state DNA NRBC b BSA(Å 2 ) c ZIF268 1aay 1.60 g.37.1.1 A Monomer B, C 13 960.81 Max 1an2 2.90 a.38.1.1 A, C Homodimer B, D 10 933.75 Papillomavirus E2 1jj4 2.40 d.58.8.1 A, B Heterodimer C, D 10 839.96 QacR 1jt0 a 2.90 a.4.1.9 B, D Homodimer E, F 12 1085.51 Lambda repressor 1lmb 1.80 a.35.1.2 3, 4 Homodimer 1, 2 10 1105.4 TATA-binding 1qn4 1.86 d.129.1.1 B Monomer E, F 15 1107.51 Tet repressor 1qpi 2.50 a.4.1.9 A, C Homodimer B, M 14 973.49 MecI 1sax 2.80 a.4.5.39 A, B Homodimer C, D 12 1130.16 Trep repressor 1tro a 1.90 a.4.12.1 A, C Homodimer I, J 12 1243.06 OhrR 1z9c 2.64 a.4.5.28 C, D Homodimer I, J 12 1669.81 Easy Phi lambda phage cII 1zs4 1.70 a.39.1.9 A, B, C, D HT d U, T 14 1043.06 p53 2ac0 1.80 b.2.5.2 A, B, C, D HT d E, F, G, H 21 1921.76 CAP 2cgp 2.20 a.4.5.4 A, F Homodimer B, C, D, E 10 944.43 LRP/ASNC family protein 2e1c 2.10 a.4.5.32 A, F Homodimer B, D 11 803.23 IdeR 2it0 a 2.60 a.4.5.24 C, D Homodimer E, F 11 1123.8 Phi 434 repressor 2or1 2.50 a.35.1.2 R, L Homodimer A, B 17 1021.78 CgmR 2yvh a 2.50 N/A C, D Homodimer E, F, G, H 10 1056.55 Controller protein 3clc a 2.80 a.35.1.3 C, D Homodimer E, F 14 1002.57 HipB 3dnv 2.68 N/A B, C Homodimer E, T 10 990.24 CprK 3e6c 1.80 a.4.5.4 C, D Homodimer A, B, E, F 12 1059.42 NrtR 3gz6 2.90 N/A A, B Homodimer C, D 15 1845.4 CopG repressor 1b01 2.56 a.43.1.3 A, B Homodimer E, F 5 573.31 RXR-alpha 1by4 2.10 g.39.1.2 A, B Homodimer E, F 8 1031.94 Met repressor 1cma 2.80 a.43.1.5 A, B Homodimer C, D 4 693.13 PhoB 1gxp a 2.50 a.4.6.1 A Monomer C, D 7 739.09 Myb 1h8a a 2.23 a.4.1.3 C Monomer D, E 8 738.59 AML1 Runt domain 1hjc 2.65 b.2.5.6 D Monomer E, F 6 540.76 MtaN 1r8d 2.70 a.6.1.3 A, B Homodimer C, D 8 1338.92 Hard Sigma subunit domain 4 1rio a 2.30 a.4.13.2 H Monomer U, T 6 423.27 Prospero 1xpx 2.80 a.4.1.1 A Monomer C, D 3 325.79 Put3 1zme 2.50 g.38.1.1 C, D Homodimer A, B 5 1211.56 Omega repressor 2bnw 2.45 a.43.1.4 A, B Homodimer E, F 4 519.26 ILF 2c6y 2.40 a.4.5.14 A Monomer C, D 8 814.94 Phi 29 protein p4 2fio 2.70 N/A A, B Homodimer C, D 4 903.33 IRF-2 2irf a 2.20 a.4.5.23 L Monomer C, D 6 668.45 PutA 2rbf 2.25 N/A A, B Homodimer C, D 8 614.12 SoxR 2zhg 2.80 a.6.1.3 A, D Homodimer B, C 6 869.73 Engrailed homeodomain 3hdd a 2.20 a.4.1.1 A Monomer C, D 4 524.73 a Has more than one binding unit b NRBC: number of protein residues having side-chain contacts with DNA bases c BSA: buried surface area in TF-DNA complexes d HT: homotetramer Results Overview of benchmark test cases There are a total of 38 test cases for our TF-DNA docking benchmarks.

Publication Year: 2011


Combinatorial targeting of ribbon-helix-helix artificial transcription factors to chimeric recognition sites.

(2012) Nucleic Acids Res 40

PubMed: 22492712 | PubMedCentral: PMC3413123 | DOI: 10.1093/nar/gks314

Indeed, the co-crystal structure of CopG with DNA (PDB 1b01) reveals that the core base specific recognition contacts span a 5′-GCAC-3′ sequence element ( 24 ).

Publication Year: 2012


CREDO: a structural interactomics database for drug discovery.

(2013) Database (Oxford) 2013

PubMed: 23868908 | PubMedCentral: PMC3715132 | DOI: 10.1093/database/bat049

For example, in PDB entry 1B01, two observed orientations (chains E and F) of the DNA part were represented as two different alternate location groups, which causes almost super-imposed residues to ha... e different identifiers in addition to completely different chemical component HET-IDs.

Publication Year: 2013


Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential.

(2005) Nucleic Acids Res 33

PubMed: 15673715 | PubMedCentral: PMC548349 | DOI: 10.1093/nar/gki204

Table 1 Data set of protein–DNA complexes Structural set (141 complexes) 1a02 1a0a 1a1g 1a1h 1a1k 1a3q 1akh 1am9 1an2 1an4 1apl 1au7 1b01 1b3t 1b72 1b8i 1bc8 1bdt 1bf5 1bl0 1by4 1c0w 1c9b 1cdw... 1cez 1cf7 1cgp 1cit 1d3u 1d5y 1ddn 1dh3 1du0 1dux 1e3o 1ea4 1efa 1egw 1f2i 1f5t 1fjl 1fos 1fzp 1g2f 1gd2 1gji 1gt0 1gu4 1gu5 1gxp 1h6f 1h8a 1h9d 1h9t 1hbx 1hcq 1hlo 1hlz 1hw2 1hwt 1ic8 1if1 1ig7 1ign 1imh 1io4 1j59 1je8 1jfi 1jgg 1jj4 1jk1 1jk2 1jnm 1jt0 1k6o 1k78 1k79 1k7a 1kb2 1kb4 1kb6 1ku7 1l3l 1lat 1lb2 1le5 1le9 1llm 1lmb 1lq1 1mdy 1mhd 1mjm 1mjo 1mm8 1mnm 1mnn 1mur 1n6j 1ngm 1nkp 1nvp 1nwq 1oct 1odh 1owf 1p47 1p7h 1pdn 1per 1pp7 1pp8 1pue 1puf 1pyi 1pzu 1r0o 1r4o 1r4r 1ram 1rio 1rpe 1run 1skn 1tf6 1tgh 1tsr 1ubd 1yrn 1ysa 1ytb 1ytf 2cgp 2drp 2gli 2hap 2hdd 2or1 6cro 6pax Table 2 Recognition accuracy for specific interactions between TFs and native bound DNA sequences Accuracy Top 1(%) Top 10(%) Top 20(%) Top 1(%) Top 5(%) Whole structural set 39.7 70.2 77.3 79.4 90.1 α-Helix a 26.3 54.4 63.2 66.7 82.5 α-Helix + β-strand a 49.4 79.2 85.7 87.0 94.8 a α-helix and β-strand refer to the secondary structures of DNA-binding sites.

Publication Year: 2005