SMTL ID : 4u6p.2 (1 other biounit)

Structural mechanism of error-free bypass of major benzo[a]pyrene adduct by human polymerase kappa

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

monomer

Ligands

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

DG-DC-DG-DG-DA-DT-DC-DA-DC.1: 34 residues within 4Å: Chain A: V.60, R.63, S.196, E.199, K.321, R.352, V.354, S.355, G.356, I.357, G.358, K.359, V.360, T.361, R.454, K.468, T.469, R.470, A.471, S.472, T.473 Chain B: G.4, G.5, T.6, G.7, A.8, T.9, C.10, C.11, G.12, C.13 Ligands: PGE.2, MG.3, DCT.6 Protein-ligand interaction information (PLIP) not available

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 7 residues within 4Å: Chain A: E.419, K.459, K.461, V.467 Chain B: G.4, G.5 Ligands: DG-DC-DG-DG-DA-DT-DC-DA-DC.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.461

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: R.352, V.354, I.357 Ligands: DG-DC-DG-DG-DA-DT-DC-DA-DC.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:R.352, A:V.354, A:I.357 MG.4: 5 residues within 4Å: Chain A: D.107, M.108, D.198 Ligands: MG.5, DCT.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.107, A:M.108, A:D.198 MG.5: 5 residues within 4Å: Chain A: D.107, D.198, E.199 Ligands: MG.4, DCT.6 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.199, H2O.1

1 x DCT: 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE(Non-covalent)

DCT.6: 16 residues within 4Å: Chain A: D.107, M.108, A.110, F.111, Y.112, S.137, T.138, Y.141, R.144, A.151, D.198, K.328 Chain B: G.4 Ligands: DG-DC-DG-DG-DA-DT-DC-DA-DC.1, MG.4, MG.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.112 Hydrogen bonds: A:A.110, A:F.111, A:T.138, A:Y.141 Salt bridges: A:R.144, A:R.144, A:K.328

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jha, V. et al., Structure and mechanism of error-free replication past the major benzo[a]pyrene adduct by human DNA polymerase kappa. Nucleic Acids Res. (2016)

Release Date

2016-01-27

Peptides

DNA polymerase kappa: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

DNA polymerase kappa

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