SMTL ID : 3fds.1

Structural insight into recruitment of translesion DNA polymerase Dpo4 to sliding clamp PCNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-1-1-1-mer

Ligands

26 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 2 residues within 4Å: Chain A: E.94, Y.95 Ligand excluded by PLIP EDO.2: 3 residues within 4Å: Chain A: G.41, P.60 Chain B: N.131 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: V.115, E.120, N.123, L.124, E.127 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: H.304 Chain B: T.151, L.152, G.154 Ligands: EDO.20 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: R.119, Y.122 Ligands: EDO.10, EDO.15 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: F.302, P.303, H.304, G.305 Ligand excluded by PLIP EDO.7: 2 residues within 4Å: Chain A: E.79, Q.83 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: V.18, L.19, V.84, R.87 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: E.100, A.102, K.148 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: Y.118, V.165, D.167 Ligands: EDO.5 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: K.137, T.139 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: Y.48, K.159, P.160 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain A: R.51, K.56 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: K.129, N.130, L.133, N.161 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: K.164, V.165 Ligands: EDO.5 Ligand excluded by PLIP EDO.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain B: V.153, E.172, K.175 Ligands: EDO.4, PEG.29 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain B: R.38, H.39, L.40, E.123 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain B: E.32, K.54, Y.60, I.62 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: N.21, T.41, L.46, M.204, D.207 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain B: T.31, D.33, G.34, I.35, F.36, R.51, P.53 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain B: E.127, K.230, D.232, I.242 Ligand excluded by PLIP EDO.26: 7 residues within 4Å: Chain B: T.137, T.138, D.139, V.142, P.186, L.187, K.188 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain B: M.220, D.232, E.234, H.240 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain B: E.173, G.174 Chain C: K.97, P.113 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain C: L.150, G.151, E.152, G.169, D.170 Ligand excluded by PLIP

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.17: 3 residues within 4Å: Chain A: Y.10, P.160, N.161 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.161 PEG.29: 11 residues within 4Å: Chain B: L.152, V.153, K.175, R.176 Chain C: D.75, D.78, I.79, F.110, E.111, L.112 Ligands: EDO.20 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:D.75, C:D.78, C:E.111, B:R.176, B:R.176

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.18: 5 residues within 4Å: Chain A: Y.122, N.123, L.126, E.127, N.130 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.123, A:E.127, A:N.130

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.19: 6 residues within 4Å: Chain A: Y.10, F.11, Y.12, T.45, I.104, D.105 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.12, A:T.45 Water bridges: A:F.11, A:F.11, A:A.44, A:D.105, A:D.105 GOL.30: 5 residues within 4Å: Chain A: K.282 Chain B: E.156, A.170, G.171, E.172 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.156, B:G.171, A:K.282 Water bridges: B:E.156 GOL.31: 7 residues within 4Å: Chain A: A.343 Chain B: V.45, Y.200, S.201, I.245, A.246, R.248 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.201, B:P.247, B:R.248 Water bridges: B:D.43, B:S.201

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.33: 9 residues within 4Å: Chain B: K.175 Chain C: G.70, F.71, K.72, D.75, L.112, P.113, L.114, I.115 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.72, C:P.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xing, G. et al., Structural insight into recruitment of translesion DNA polymerase Dpo4 to sliding clamp PCNA. Mol.Microbiol. (2009)

Release Date

2009-01-20

Peptides

DNA polymerase IV: A
DNA polymerase sliding clamp B: B
DNA polymerase sliding clamp C: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

DNA polymerase IV

DNA polymerase sliding clamp B

DNA polymerase sliding clamp C

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