SMTL ID : 5wm8.1

Structure of the 10R (+)-cis-BP-dG modified Rev1 ternary complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 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.11 MG.3: 6 residues within 4Å: Chain A: G.12 Chain C: D.58, D.163, E.164 Ligands: MG.4, DCP.6 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.163, C:D.163, C:E.164 MG.4: 6 residues within 4Å: Chain C: D.58, F.59, D.163 Ligands: MG.3, MG.5, DCP.6 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.58, C:F.59, C:D.163 MG.5: 4 residues within 4Å: Chain C: D.58, K.221 Ligands: MG.4, DCP.6 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.58, H2O.7, H2O.10, H2O.10

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

BAP.2: 8 residues within 4Å: Chain B: G.5 Chain C: D.95, W.113, H.251, K.377, M.381 Ligands: EDO.13, PEG.19 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.95, C:K.377

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

DCP.6: 20 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.3, MG.4, MG.5, GOL.9 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:N.110 Water bridges: C:R.104, C:R.104, C:R.104 Salt bridges: C:R.104, C:R.104, C:K.221

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain C: W.27, N.30, L.31, Q.138, S.141, E.142, I.162 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:W.27, C:S.141 Water bridges: C:K.34, C:K.34 GOL.8: 7 residues within 4Å: Chain C: L.31, K.34, F.35, E.38, Y.145, I.157, P.159 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:L.31, C:F.35, C:I.157 Water bridges: C:K.34, C:K.34 GOL.9: 8 residues within 4Å: Chain A: A.11, G.12 Chain B: C.6 Chain C: R.20, L.21, D.95, G.111 Ligands: DCP.6 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.20, C:D.95, C:D.95

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

EDO.10: 7 residues within 4Å: Chain B: T.3, C.4 Chain C: V.4, F.11, S.14, Y.15, W.325 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.4, C:S.14, C:S.14 EDO.11: 5 residues within 4Å: Chain A: T.7 Chain C: F.387, S.388, R.389, L.414 No protein-ligand interaction detected (PLIP) EDO.12: 4 residues within 4Å: Chain C: R.190, F.194, 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:C.200 EDO.13: 5 residues within 4Å: Chain C: M.112, W.113, Q.116 Ligands: BAP.2, PEG.19 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:W.113 EDO.14: 5 residues within 4Å: Chain C: D.60, C.61, F.80, T.201, P.222 2 PLIP interactions: 2 interactions with chain C Water bridges: C:K.81, C:K.81 EDO.15: 8 residues within 4Å: Chain B: T.7, A.8 Chain C: F.16, H.22, L.319, S.320, I.321, Y.345 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:H.22, C:R.316, C:S.320, C:Y.345 Water bridges: C:R.316 EDO.16: 5 residues within 4Å: Chain C: S.74, F.75, S.76, A.77, C.78 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.77 EDO.17: 4 residues within 4Å: Chain B: C.9 Chain C: S.318, Q.427, N.429 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.318, C:Q.427, C:N.429 EDO.18: 2 residues within 4Å: Chain C: T.47, D.48 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.48

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

PEG.19: 3 residues within 4Å: Chain C: W.113 Ligands: BAP.2, EDO.13 No protein-ligand interaction detected (PLIP) PEG.20: 3 residues within 4Å: Chain C: Q.195, N.198, G.199 No protein-ligand interaction detected (PLIP)

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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