SMTL ID : 6brx.2 (1 other biounit)

Crystal Structure of Human DNA polymerase kappa in complex with DNA containing the major cisplatin lesion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

1 x DT- DA- DC- DA- DT- DA- DC- DA- DC: DNA (5'-D(P*TP*AP*CP*AP*TP*AP*CP*AP*C)-3')(Non-covalent)

DT-DA-DC-DA-DT-DA-DC-DA-DC.1: 32 residues within 4Å: Chain A: V.85, R.88, S.221, D.223, E.224, K.346, V.379, S.380, G.381, I.382, G.383, K.384, V.385, T.386, R.479, K.493, T.494, R.495, A.496, S.497, T.498 Chain B: G.5, T.6, G.7, T.8, A.9, T.10, G.11, T.12, A.13 Ligands: 0KX.3, MG.4 Protein-ligand interaction information (PLIP) not available

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.132, M.133, D.223 Ligands: 0KX.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.132, A:M.133, A:D.223 MG.4: 5 residues within 4Å: Chain A: R.377, V.379, G.381, I.382 Ligands: DT-DA-DC-DA-DT-DA-DC-DA-DC.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:R.377, A:V.379, A:I.382

1 x 0KX: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine(Non-covalent)

0KX.3: 17 residues within 4Å: Chain A: D.132, M.133, D.134, A.135, F.136, Y.137, S.162, T.163, Y.166, R.169, D.223, E.224, K.353 Chain B: G.4 Ligands: DT-DA-DC-DA-DT-DA-DC-DA-DC.1, MG.2, PEG.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.137 Hydrogen bonds: A:D.132, A:A.135, A:F.136, A:Y.137, A:Y.166, A:Y.166, A:R.169, A:D.223 Salt bridges: A:R.169, A:K.353

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

PEG.5: 3 residues within 4Å: Chain B: G.4, G.5 Ligands: 0KX.3 No protein-ligand interaction detected (PLIP)

1 x CPT: Cisplatin(Non-functional Binders)

CPT.6: 2 residues within 4Å: Chain B: G.4, G.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jha, V. et al., Structural Basis for Human DNA Polymerase Kappa to Bypass Cisplatin Intrastrand Cross-Link (Pt-GG) Lesion as an Efficient and Accurate Extender. J. Mol. Biol. (2018)

Release Date

2018-08-22

Peptides

DNA polymerase kappa: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

DNA polymerase kappa

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