SMTL ID : 6brx.1 (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: 35 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, V.492, 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: MG.3, MG.4, 0KX.5, PEG.6 Protein-ligand interaction information (PLIP) not available

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.132, M.133, D.223 Ligands: MG.4, 0KX.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.132, A:M.133, A:D.223 MG.3: 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 MG.4: 6 residues within 4Å: Chain A: D.132, D.223, E.224 Ligands: DT-DA-DC-DA-DT-DA-DC-DA-DC.1, MG.2, 0KX.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.223, A:E.224

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

0KX.5: 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, K.353 Chain B: G.4 Ligands: DT-DA-DC-DA-DT-DA-DC-DA-DC.1, MG.2, MG.4, PEG.6 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.137, A:T.163 Hydrogen bonds: A:A.135, A:F.136, A:Y.137, A:T.163, A:R.169 Water bridges: A:T.163, A:Y.166, A:D.350 Salt bridges: A:R.169, A:K.353

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

PEG.6: 4 residues within 4Å: Chain B: G.4, G.5 Ligands: DT-DA-DC-DA-DT-DA-DC-DA-DC.1, 0KX.5 No protein-ligand interaction detected (PLIP)

1 x CPT: Cisplatin(Non-functional Binders)

CPT.7: 3 residues within 4Å: Chain B: G.4, G.5, T.6 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
A

DNA polymerase kappa

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