SMTL ID : 6pl8.1

Structure of human DNA polymerase eta complexed with 8OA in the template base paired with incoming non-hydrolyzable TTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 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: 28 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, R.380, L.381, L.384, R.385, R.386, C.387 Chain B: A.4, A.5, T.6, G.7, A.8, C.9, G.10, C.11, T.12 Ligands: 1FZ.2, MG.4 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:I.50, A:R.64, A:S.65, A:R.96, A:K.320, A:T.321, A:G.323, A:S.325, A:N.327, A:R.354 Water bridges: A:R.96 Salt bridges: A:K.89, A:R.96, A:K.296, A:K.314, A:R.316, A:K.320, A:K.326, A:R.354

1 x 1FZ: 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine(Non-covalent)

1FZ.2: 19 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, D.118, K.234 Chain B: T.3, A.4, A.5 Ligands: DA-DG-DC-DG-DT-DC-DA-DT.1, MG.3, MG.4 10 PLIP interactions: 10 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 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: 1FZ.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-DC-DG-DT-DC-DA-DT.1, 1FZ.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.2

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 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 Hydrogen bonds: A:F.250 Water bridges: A:E.280

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koag, M.C. et al., Structure of human DNA polymerase eta complexed with 8OA in the template base paired with incoming non-hydrolyzable TTP. To Be Published

Release Date

2020-07-01

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase eta

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