SMTL ID : 4u7c.1 (1 other biounit)

Structure of DNA polymerase kappa in complex with benzopyrene adducted DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

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

DG-DC-DG-DG-DA-DT-DC-DA-DG.1: 30 residues within 4Å: Chain A: R.37, S.170, D.172, E.173, K.295, G.330, I.331, G.332, K.333, V.334, T.335, R.428, K.442, T.443, R.444, A.445, S.446, T.447 Chain B: X.4, C.5, T.6, G.7, A.8, T.9, C.10, C.11, G.12, C.13 Ligands: 0KX.3, PEG.4 Protein-ligand interaction information (PLIP) not available

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.81, M.82, D.172 Ligands: 0KX.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.81, A:M.82, A:D.172

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.81, M.82, D.83, A.84, F.85, Y.86, S.111, T.112, Y.115, R.118, A.125, D.172, E.173, K.302 Chain B: X.4 Ligands: DG-DC-DG-DG-DA-DT-DC-DA-DG.1, MG.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.86 Hydrogen bonds: A:A.84, A:F.85, A:Y.86, A:Y.115, A:R.118 Salt bridges: A:R.118, A:K.302

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

PEG.4: 5 residues within 4Å: Chain A: K.433, K.435, V.441 Ligands: DG-DC-DG-DG-DA-DT-DC-DA-DG.1, DG-DC-DG-DG-DA-DT-DC-DA-DG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.433

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
A

DNA polymerase kappa

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