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PDB ID Mentions in PubMed Central Article count: 3

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PDB ID Mentions in PubMed Central

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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.

(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


The bacterial antitoxin HipB establishes a ternary complex with operator DNA and phosphorylated toxin HipA to regulate bacterial persistence.

(2014) Nucleic Acids Res 42

PubMed: 25056321 | PubMedCentral: PMC4150777 | DOI: 10.1093/nar/gku665

Unexpectedly, the overall HipAB so :DNA complex assembly is remarkably distinct from the previously characterized E. coli HipAB so :DNA ternary complex (PDB:3DNV) ( 14 ) (Figure 2b ).

( b ) X-ray crystal structure of the E.coli HipAB:DNA complex (PDB: 3DNV) in top view oriented based on a superposition with duplex DNA and HipB so shown in panel (a).

To determine the structure of HipB so , the S. oneidensis MR-1 HipB so sequence and a subunit from the crystal structure of dimeric E. coli HipB (PDB: 3DNV) were used to create a truncated search model lacking loop regions and non-conserved side chains using CCP4 Chainsaw.

Publication Year: 2014


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4360534

Schumacher MA , 2008 , MDT Protein , 3DNV ; http://dx.doi.org/10.2210/pdb3DNV/pdb , Publicly available at the RCSB Protein Data Bank.

Publication Year: 2014