SMTL ID : 2r8j.2 (1 other biounit)

Structure of the Eukaryotic DNA Polymerase eta in complex with 1,2-d(GpG)-cisplatin containing DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

monomer

Ligands

1 x DG- DT- DG- DG- DA- DT- DG- DA- DG: DNA (5'-D(*DGP*DTP*DGP*DGP*DAP*DTP*DGP*DAP*DG)-3')(Non-covalent)

DG-DT-DG-DG-DA-DT-DG-DA-DG.1: 17 residues within 4Å: Chain A: C.3, T.4, C.5, A.6, T.7, C.8, C.9, A.10, C.11 Chain B: S.176, I.177, G.333, V.334, N.384, R.479 Ligands: CPT.2, DCP.5 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:Q.78, B:R.96, B:R.96, B:K.416, B:S.417, B:M.419, B:M.419, B:N.421, B:N.421 Water bridges: B:N.423, B:N.423 Salt bridges: B:K.148, B:K.416, B:K.416, B:R.449

1 x CPT: Cisplatin(Non-functional Binders)

CPT.2: 4 residues within 4Å: Chain A: G.1, G.2, C.3 Ligands: DG-DT-DG-DG-DA-DT-DG-DA-DG.1 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain B: D.53, D.178, E.179 Ligands: CA.4, DCP.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.53, B:D.178, B:D.178, B:E.179 CA.4: 5 residues within 4Å: Chain B: D.53, M.54, D.178 Ligands: CA.3, DCP.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.53, B:D.53, B:M.54, B:D.178

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

DCP.5: 17 residues within 4Å: Chain A: G.2, C.3 Chain B: D.53, M.54, N.55, A.56, F.57, F.58, I.83, Y.87, R.90, R.96, D.178, K.302 Ligands: DG-DT-DG-DG-DA-DT-DG-DA-DG.1, CA.3, CA.4 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:M.54, B:A.56, B:F.57, B:F.58, B:R.90 Water bridges: B:V.85, B:R.90, B:R.90, B:K.302 Salt bridges: B:R.90, B:R.96, B:R.96, B:K.302

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alt, A. et al., Bypass of DNA lesions generated during anticancer treatment with cisplatin by DNA polymerase eta. Science (2007)

Release Date

2007-12-11

Peptides

DNA polymerase eta: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
B

DNA polymerase eta

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