SMTL ID : 7rbh.1

Human DNA polymerase beta crosslinked ternary complex 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x DG- DT- DC- DG- DG: DNA (5'-D(*GP*TP*CP*GP*G)-3')(Non-covalent)

DG-DT-DC-DG-DG.1: 18 residues within 4Å: Chain A: H.34, K.35, A.38, Y.39, L.62, P.63, G.64, V.65, G.66, T.67, K.68, I.69 Chain C: C.1, C.2, G.3, A.4, C.5 Ligands: QPJ.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.280, A:R.283, A:R.283 Water bridges: A:N.37 Salt bridges: A:K.280 pi-Stacking: A:H.34

1 x QPJ: 2-deoxy-3,5-di-O-phosphono-D-erythro-pentitol(Covalent)

QPJ.2: 6 residues within 4Å: Chain A: K.35, Y.39, K.68, K.72, K.84 Ligands: DG-DT-DC-DG-DG.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:K.72 Hydrogen bonds: A:K.68 Water bridges: A:K.84, A:K.84 Salt bridges: A:K.35, A:K.68, A:K.84

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

DCP.3: 18 residues within 4Å: Chain A: G.179, S.180, R.183, S.188, G.189, D.190, D.192, Y.271, F.272, T.273, G.274, S.275, D.276, N.279 Chain B: C.10 Chain C: G.6 Ligands: CA.4, CA.5 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:D.276 Hydrogen bonds: A:R.149, A:S.180, A:S.180, A:R.183, A:G.189, A:D.190, A:D.190, A:D.192, A:N.279 Water bridges: A:F.181, A:F.181, A:R.183, A:D.276 Salt bridges: A:R.183 DCP.7: 1 residues within 4Å: Chain C: C.2 No protein-ligand interaction detected (PLIP)

3 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: D.190, D.192 Ligands: DCP.3, CA.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.190, A:D.192, H2O.1 CA.5: 6 residues within 4Å: Chain A: D.190, D.192, D.256 Chain B: C.10 Ligands: DCP.3, CA.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.190, A:D.192, A:D.256, H2O.10 CA.6: 4 residues within 4Å: Chain A: R.283, E.295 Chain C: G.7, C.8 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.295

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, A. et al., Interlocking activities of DNA polymerase beta in the base excision repair pathway. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-03-09

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase beta

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