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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.

Publication Year: 2011