SMTL ID : 5wm1.1

Structure of the 10S (+)-trans-BP-dG modified Rev1 ternary complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 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.3 MG.4: 7 residues within 4Å: Chain A: G.12 Chain C: D.58, D.163, E.164 Ligands: MG.5, MG.6, DCP.7 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.163, C:D.163, C:E.164 MG.5: 7 residues within 4Å: Chain C: D.58, F.59, D.163, K.221 Ligands: MG.4, MG.6, DCP.7 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.58, C:F.59, C:D.163 MG.6: 5 residues within 4Å: Chain C: D.58, K.221 Ligands: MG.4, MG.5, DCP.7 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.58, H2O.7, H2O.11, H2O.12

1 x BAP: 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE(Non-covalent)

BAP.2: 5 residues within 4Å: Chain B: G.5 Chain C: H.251, M.381 Ligands: EDO.3, GOL.10 No protein-ligand interaction detected (PLIP)

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

EDO.3: 3 residues within 4Å: Chain B: G.5 Chain C: G.382 Ligands: BAP.2 No protein-ligand interaction detected (PLIP) EDO.13: 4 residues within 4Å: Chain C: K.218, S.240, K.242, D.245 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.245 Water bridges: C:K.218, C:M.219 EDO.14: 3 residues within 4Å: Chain C: T.47, D.48, Y.308 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.48 EDO.15: 4 residues within 4Å: Chain C: W.27, N.30, L.31, K.34 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.30, C:K.34 EDO.16: 5 residues within 4Å: Chain C: I.53, I.171, T.178, D.208, F.229 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.178, C:D.208 Water bridges: C:I.175, C:I.175 EDO.17: 5 residues within 4Å: Chain C: D.60, C.61, F.80, T.201, P.222 1 PLIP interactions: 1 interactions with chain C Water bridges: C:T.65 EDO.18: 3 residues within 4Å: Chain C: F.194, Q.195, N.198 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.198 EDO.19: 4 residues within 4Å: Chain B: C.4 Chain C: V.4, S.14, Y.15 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.4, C:S.14, C:S.14

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

DCP.7: 20 residues within 4Å: Chain A: G.12 Chain C: R.20, L.21, 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.4, MG.5, MG.6 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:F.63 Hydrogen bonds: C:R.20, C:D.58, C:C.61, C:F.62, C:F.63, C:S.98, C:S.98, C:N.110, C:D.163 Water bridges: C:R.104, C:R.104, C:R.104 Salt bridges: C:R.104, C:R.104, C:K.221

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 5 residues within 4Å: Chain C: D.50, 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.9: 5 residues within 4Å: Chain C: R.190, Q.191, F.194, T.201, N.223 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.223, C:N.223 Water bridges: C:Q.191, C:V.202 GOL.10: 5 residues within 4Å: Chain B: G.5 Chain C: D.95, W.113, K.377 Ligands: BAP.2 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.95, C:K.377 GOL.11: 7 residues within 4Å: Chain C: L.31, K.34, F.35, E.38, Y.145, I.157, P.159 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:F.35, C:E.38, C:I.157 Water bridges: C:K.34 GOL.12: 5 residues within 4Å: Chain C: S.239, S.266, N.268, D.269, K.272 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.266, C:N.268, C:K.272 Water bridges: C:E.235, C:K.272

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

PEG.20: 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

Related Entries With Identical Sequence