SMTL ID : 6x71.1

Rev1 Mg2+-facilitated Intermediate complex with reactant dCTP and product dCMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

monomer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: A.11, G.12, C.13 Chain B: C.6 Chain C: R.20, 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 GOL.8: 8 residues within 4Å: Chain C: W.27, N.30, L.31, Q.138, S.141, E.142, Y.145, I.162 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:W.27, C:L.31, C:Q.138, C:S.141 Water bridges: C:N.30 GOL.9: 6 residues within 4Å: Chain C: L.31, K.34, F.35, E.38, Y.145, P.159 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:L.31, C:F.35, C:E.38 Water bridges: C:K.34, C:K.34, C:K.34, C:E.38

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 8 residues within 4Å: Chain A: G.12, C.13 Chain C: D.58, S.161, D.163, E.164 Ligands: MG.3, DCP.6 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.58, C:D.163, C:E.164, H2O.14 MG.3: 7 residues within 4Å: Chain A: C.13 Chain C: D.58, F.59, D.163 Ligands: MG.2, DCP.6, POP.7 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.58, C:F.59, C:D.163 MG.4: 6 residues within 4Å: Chain A: C.13 Chain C: D.58, R.214, K.221 Ligands: DCP.6, POP.7 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain A: A.11 Chain C: D.244, L.246, V.249 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.244, C:L.246, H2O.5, H2O.14

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

DCP.6: 23 residues within 4Å: Chain A: G.12, C.13 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, G.111, D.163, K.221 Ligands: GOL.1, MG.2, MG.3, MG.4, POP.7 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:F.63, C:N.110 Hydrogen bonds: C:R.20, C:F.59, C:C.61, C:F.62, C:F.63, C:S.98, C:S.98, C:Y.101, C:Y.101, C:N.110, C:D.163 Water bridges: C:D.58, C:R.104, C:R.104, C:R.104, C:R.214 Salt bridges: C:R.104, C:R.104, C:K.221

1 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.7: 15 residues within 4Å: Chain A: C.13 Chain C: D.58, F.59, D.60, C.61, F.62, S.98, Y.101, R.104, N.110, D.163, K.221 Ligands: MG.3, MG.4, DCP.6 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:F.59, C:C.61, C:F.62, C:Y.101, C:Y.101, 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weaver, T.M. et al., Visualizing Rev1 catalyze protein-template DNA synthesis. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-09-30

Peptides

DNA repair protein REV1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA repair protein REV1

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