SMTL ID : 6m7t.1

Human DNA polymerase eta in a non-productive ternary complex with Ca2+ and dTTP oppositing cdA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

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

DA-DG-DT-DG-DT-DG-DA-DG.1: 23 residues within 4Å: Chain A: S.116, D.118, E.119, Y.121, K.227, I.258, R.259, S.260, L.261, G.262, G.263, K.264, L.265, R.380, R.385 Chain B: A.1, C.4, T.5, C.6, A.7, C.8, A.9, C.10 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:K.320, A:T.321, A:T.321, A:G.323, A:S.325, A:N.327, A:N.327 Water bridges: A:K.314, A:G.323 Salt bridges: A:K.89, A:K.296, A:K.320, A:K.326, A:R.354

1 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 2 residues within 4Å: Chain A: H.396, H.400 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.396, A:H.400

1 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.3: 15 residues within 4Å: Chain A: D.16, M.17, D.18, C.19, F.20, F.21, I.51, Y.55, R.58, R.64, D.118, K.234 Chain B: A.1, X.3 Ligands: CA.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.21 Hydrogen bonds: A:M.17, A:D.18, A:C.19, A:F.20, A:F.21 Salt bridges: A:R.58, A:R.64, A:R.64, A:K.234 pi-Cation interactions: A:R.64

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: D.16, M.17, D.118 Ligands: TTP.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.16, A:M.17, A:D.118

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

EDO.5: 3 residues within 4Å: Chain A: V.370, R.385, F.426 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.385

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: T.285, E.286, S.287, Y.302 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.285, A:T.285, A:E.286, A:S.287 GOL.7: 5 residues within 4Å: Chain A: S.260, L.265, K.296, N.297, W.300 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.260, A:S.260, A:K.296 GOL.8: 3 residues within 4Å: Chain A: Q.283, F.284, Q.288 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.283, A:Q.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weng, P.J. et al., Bypassing a 8,5'-cyclo-2'-deoxyadenosine lesion by human DNA polymerase eta at atomic resolution. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-09-12

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase eta

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