SMTL ID : 4q8e.1

Human DNA polymerase eta inserting dCMPNPP opposite a phenanthriplatin adducted G

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

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

DA-DG-DT-DG-DT-DG-DA-DG.1: 27 residues within 4Å: Chain A: S.116, D.118, E.119, K.227, I.258, R.259, S.260, L.261, G.262, G.263, K.264, L.265, R.380, R.385, R.386, C.387 Chain B: X.2, C.3, T.4, C.5, A.6, C.7, A.8, C.9, T.10 Ligands: 0KX.2, MG.4 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:W.67 Hydrogen bonds: A:Q.41, A:K.320, A:T.321, A:G.323, A:S.325, A:N.327, A:R.354 Water bridges: A:A.90, A:A.90, A:R.96, A:R.96, A:R.114, A:R.114, A:R.114, A:R.114, A:R.114, A:K.296, A:R.316, A:T.321, A:R.354, A:R.354 Salt bridges: A:K.89, A:R.96, A:R.96, A:K.296, A:K.296, A:R.316, A:K.320, A:K.326, A:R.354

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

0KX.2: 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: X.2 Ligands: DA-DG-DT-DG-DT-DG-DA-DG.1, MG.3, MG.4 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.21 Hydrogen bonds: A:C.19, A:F.20, A:F.21, A:Y.55, A:Y.55, A:R.58, A:R.64, A:R.64 Water bridges: A:Y.55, A:R.58, A:R.58 Salt bridges: A:R.58, A:K.234

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: D.16, M.17, D.118, K.234 Ligands: 0KX.2, MG.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.16, A:M.17, A:D.118 MG.4: 7 residues within 4Å: Chain A: D.16, S.116, D.118, E.119 Ligands: DA-DG-DT-DG-DT-DG-DA-DG.1, 0KX.2, MG.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.16, A:D.118, A:E.119, H2O.13

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: P.247, F.250, S.251, G.279, E.280 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.282, A:T.282 GOL.6: 3 residues within 4Å: Chain A: E.97, A.98, E.101 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.101 Water bridges: A:R.27, A:E.97 GOL.7: 3 residues within 4Å: Chain A: N.29, P.30, H.31 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gregory, M.T. et al., Structural and mechanistic studies of polymerase eta bypass of phenanthriplatin DNA damage. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-07-02

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase eta

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