SMTL ID : 5t14.2 (1 other biounit)

DNA polymerase kappa extending beyond a bulky major benzo[a]pyrene adduct

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

monomer

Ligands

1 x DC- DG- DG- DA- DT- DC- DG- DA- DC: DNA(Non-covalent)

DC-DG-DG-DA-DT-DC-DG-DA-DC.1: 34 residues within 4Å: Chain A: K.56, V.60, R.63, S.196, D.198, E.199, K.321, 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: T.4, X.5, T.6, C.7, G.8, A.9, T.10, C.11, C.12, G.13 Ligands: MG.4, DZ4.5 Protein-ligand interaction information (PLIP) not available

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

PGE.2: 3 residues within 4Å: Chain A: A.428, Y.432, K.489 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.432

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.107, M.108, D.198, K.328 Ligands: DZ4.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.107, A:M.108, A:D.198 MG.4: 6 residues within 4Å: Chain A: R.352, V.354, S.355, G.356, I.357 Ligands: DC-DG-DG-DA-DT-DC-DG-DA-DC.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:R.352, A:V.354, A:I.357

1 x DZ4: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine(Non-covalent)

DZ4.5: 17 residues within 4Å: Chain A: D.107, M.108, D.109, A.110, F.111, Y.112, S.137, T.138, Y.141, R.144, A.150, A.151, D.198, K.328 Chain B: T.4 Ligands: DC-DG-DG-DA-DT-DC-DG-DA-DC.1, MG.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.112 Hydrogen bonds: A:A.110, A:F.111, A:Y.112, A:Y.141, A:R.144, A:D.198 Water bridges: A:Y.112, A:E.199, A:E.199 Salt bridges: A:R.144, A:K.328

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jha, V. et al., Structural basis of accurate replication beyond a bulky major benzo[a]pyrene adduct by human DNA polymerase kappa. DNA Repair (Amst.) (2017)

Release Date

2016-12-21

Peptides

DNA polymerase kappa: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

DNA polymerase kappa

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