SMTL ID : 5wmb.1

Structure of the 10S (-)-cis-BP-dG modified Rev1 ternary complex (the BP residue is disordered)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: A.11 Chain C: D.244, L.246, V.249 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.244, C:L.246, C:V.249, H2O.1, H2O.2 MG.2: 7 residues within 4Å: Chain A: G.12 Chain C: D.58, D.163, E.164 Ligands: MG.3, MG.4, DCP.5 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.58, C:D.163, C:D.163, C:E.164 MG.3: 6 residues within 4Å: Chain C: D.58, F.59, D.163 Ligands: MG.2, MG.4, DCP.5 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.58, C:F.59, C:D.163 MG.4: 5 residues within 4Å: Chain C: D.58, K.221 Ligands: MG.2, MG.3, DCP.5 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.58, H2O.4, H2O.5, H2O.6

1 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

DCP.5: 19 residues within 4Å: Chain A: G.12 Chain C: R.20, L.24, D.58, F.59, D.60, C.61, F.62, F.63, A.97, S.98, Y.101, R.104, N.110, D.163, K.221 Ligands: MG.2, MG.3, MG.4 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:F.63 Hydrogen bonds: C:R.20, C:C.61, C:F.62, C:F.63, C:S.98, C:S.98, C:Y.101, C:N.110 Water bridges: C:R.104 Salt bridges: C:R.104, C:R.104, C:K.221

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain C: T.51, Y.52, D.208, K.230 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.52, C:K.230, C:K.230 GOL.7: 4 residues within 4Å: Chain C: R.190, Q.191, T.201, N.223 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.190, C:R.190, C:N.223 Water bridges: C:R.190, C:V.202 GOL.8: 8 residues within 4Å: Chain C: L.31, K.34, F.35, E.38, Y.145, K.149, I.157, P.159 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:L.31, C:F.35, C:K.149 Water bridges: C:K.34, C:K.34 GOL.9: 5 residues within 4Å: Chain C: S.239, S.266, N.268, D.269, K.272 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.266, C:N.268 Water bridges: C:K.272

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

EDO.10: 4 residues within 4Å: Chain C: K.218, S.240, K.242, D.245 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.242, C:D.245 EDO.11: 3 residues within 4Å: Chain C: T.47, D.48, Y.308 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.48, C:D.48 EDO.12: 7 residues within 4Å: Chain C: W.27, N.30, L.31, Q.138, S.141, E.142, I.162 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:W.27 Water bridges: C:K.34, C:K.34 EDO.13: 5 residues within 4Å: Chain C: I.171, T.178, D.208, F.229, S.231 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.178, C:S.231, C:S.231 EDO.14: 3 residues within 4Å: Chain C: C.61, F.80, N.223 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.65, C:T.65, C:N.223 EDO.15: 3 residues within 4Å: Chain C: F.194, N.198, G.199 2 PLIP interactions: 2 interactions with chain C Water bridges: C:Q.195, C:N.198 EDO.16: 5 residues within 4Å: Chain B: C.4 Chain C: V.4, F.11, S.14, Y.15 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.4, C:S.14

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

PEG.17: 3 residues within 4Å: Chain C: S.391, R.392, E.406 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.392

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rechkoblit, O. et al., Mechanism of error-free replication across benzo[a]pyrene stereoisomers by Rev1 DNA polymerase. Nat Commun (2017)

Release Date

2017-10-25

Peptides

DNA repair protein REV1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA repair protein REV1

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