SMTL ID : 5dlf.1

Crystal Structure of Human DNA Polymerase Eta Inserting dATP Opposite O4-Methylhymidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

monomer

Ligands

1 x DA- DG- DC- DG- DT- DC- DA- DT: DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3')(Non-covalent)

DA-DG-DC-DG-DT-DC-DA-DT.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, S.382, L.384, R.385, R.386, C.387 Chain B: A.5, T.6, G.7, A.8, C.9, G.10, C.11, T.12 Ligands: DTP.2 Protein-ligand interaction information (PLIP) not available

1 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.2: 17 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: A.5 Ligands: DA-DG-DC-DG-DT-DC-DA-DT.1, CA.3 18 PLIP interactions: 18 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 Water bridges: A:D.18, A:Q.41, A:R.58, A:R.58, A:R.64, A:R.64, A:K.234 Salt bridges: A:R.58, A:R.58, A:R.64, A:R.64, A:K.234

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.16, M.17, D.118 Ligands: DTP.2 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: 6 residues within 4Å: Chain A: P.247, F.250, S.251, G.279, E.280, T.282 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.282, A:T.282

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

O'Flaherty, D.K. et al., Lesion Orientation ofO4-Alkylthymidine Influences Replication by Human DNA Polymeraseeta. Chem Sci (2016)

Release Date

2016-08-10

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase eta

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