SMTL ID : 4dl4.1

Human DNA polymerase eta inserting dCMPNPP opposite the 3'G of cisplatin crosslinked Gs (Pt-GG1).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

DT-DA-DG-DT-DG-DT-DG-DA-DG.1: 29 residues within 4Å: Chain A: S.116, D.118, E.119, K.227, R.259, S.260, L.261, G.262, G.263, K.264, L.265, Q.368, R.380, L.384, R.385, R.386, C.387, K.431 Chain B: G.2, C.3, T.4, C.5, A.6, C.7, A.8, C.9, T.10 Ligands: MG.2, 0KX.6 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:W.67 Hydrogen bonds: A:Q.41, A:I.50, A:I.50, A:K.320, A:T.321, A:G.323, A:S.325, A:N.327, A:N.327, A:R.354 Water bridges: A:Q.41, A:R.96, A:K.314 Salt bridges: A:K.89, A:R.96, A:R.96, A:K.296, A:R.316, A:K.320, A:K.326, A:R.354

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: D.16, D.118, E.119 Ligands: DT-DA-DG-DT-DG-DT-DG-DA-DG.1, MG.3, 0KX.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.16, A:D.118, A:E.119, H2O.1 MG.3: 6 residues within 4Å: Chain A: D.16, M.17, D.118, K.234 Ligands: MG.2, 0KX.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.16, A:M.17, A:D.118

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: P.247, F.250, S.251, G.279, E.280 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.250 Water bridges: A:T.282

1 x CPT: Cisplatin(Non-functional Binders)

CPT.5: 3 residues within 4Å: Chain B: G.1, G.2, C.3 No protein-ligand interaction detected (PLIP)

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

0KX.6: 18 residues within 4Å: Chain A: D.16, M.17, D.18, C.19, F.20, F.21, I.51, A.52, Y.55, R.58, R.64, I.117, D.118, K.234 Chain B: G.2 Ligands: DT-DA-DG-DT-DG-DT-DG-DA-DG.1, MG.2, MG.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.21 Hydrogen bonds: A:D.18, A:C.19, A:F.20, A:F.21, A:Y.55, A:R.58, A:R.64 Water bridges: A:D.16, A:Y.55, A:R.58, A:R.58 Salt bridges: A:R.58, A:K.234 pi-Cation interactions: A:R.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Y. et al., Structural Basis for Chemoresistance to Cisplatin Mediated by DNA Polymerase eta. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2012-05-09

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase eta

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