SMTL ID : 5w2c.1 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

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

DC-DG-DG-DA-DT-DC-DG-DA-DC.1: 34 residues within 4Å: Chain A: Q.84, 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, K.493, T.494, R.495, A.496, S.497, T.498 Chain B: X.5, T.6, C.7, G.8, A.9, T.10, C.11, C.12, G.13 Ligands: MG.3, MG.4, DZ4.9 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, K.353 Ligands: DZ4.9 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.132, A:M.133, A:D.223 MG.3: 4 residues within 4Å: Chain A: R.377, V.379, I.382 Ligands: DC-DG-DG-DA-DT-DC-DG-DA-DC.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:R.377, A:V.379, A:I.382, H2O.1 MG.4: 5 residues within 4Å: Chain A: D.132, D.223, E.224 Ligands: DC-DG-DG-DA-DT-DC-DG-DA-DC.1, DZ4.9 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.223, A:E.224

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 2 residues within 4Å: Chain A: F.196 Chain B: X.5 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.137

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 4 residues within 4Å: Chain A: M.142, N.165, Y.166, H.167 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.166 Water bridges: A:D.150 EDO.7: 2 residues within 4Å: Chain A: Y.457, K.514 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.514

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

PEG.8: 2 residues within 4Å: Chain A: E.327, N.355 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.355

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

DZ4.9: 18 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, A.175, D.223, K.353 Chain B: T.4, X.5 Ligands: DC-DG-DG-DA-DT-DC-DG-DA-DC.1, MG.2, MG.4 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.137, A:T.163 Hydrogen bonds: A:D.132, A:D.134, A:A.135, A:F.136, A:Y.137, A:T.163, A:T.163, A:Y.166, A:R.169 Water bridges: A:R.169, A:R.169, A:D.223 Salt bridges: A:R.169, A:K.353

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
A

DNA polymerase kappa

Related Entries With Identical Sequence