SMTL ID : 5w2a.2 (1 other biounit)

Structure of human DNA polymerase kappa in complex with Lucidin-derived DNA adduct and incoming dCMPNPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 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: 34 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, T.480, K.493, T.494, R.495, A.496, S.497, T.498 Chain B: X.4, C.5, T.6, G.7, A.8, T.9, C.10, C.11, G.12, C.13 Ligands: 0KX.5, GOL.7 Protein-ligand interaction information (PLIP) not available

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.132, M.133, D.223 Ligands: 0KX.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.132, A:M.133, A:D.223

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: Y.457, K.514, E.515, K.518 No protein-ligand interaction detected (PLIP) GOL.4: 3 residues within 4Å: Chain A: M.218, Y.226, S.429 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.429, A:T.433 GOL.7: 5 residues within 4Å: Chain A: M.220 Chain B: X.4, T.6 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:M.220

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

0KX.5: 16 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: X.4 Ligands: DG-DC-DG-DG-DA-DT-DC-DA-DG.1, MG.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.137, A:S.162 Hydrogen bonds: A:A.135, A:F.136, A:Y.137, A:Y.166, A:R.169 Salt bridges: A:R.169, A:K.353

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

PGE.6: 4 residues within 4Å: Chain A: F.196, R.200, L.222 Chain B: X.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yockey, O.P. et al., Mechanism of Error-Free DNA Replication Past Lucidin-Derived DNA Damage by Human DNA Polymerase kappa. Chem. Res. Toxicol. (2017)

Release Date

2017-10-18

Peptides

DNA polymerase kappa: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

DNA polymerase kappa

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