SMTL ID : 6mxo.1

Structure of HPoleta incorporating dCTP opposite the 3-prime Pt(DACH)-GG

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.04 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: 30 residues within 4Å: Chain A: S.120, D.122, E.123, K.231, R.263, S.264, L.265, G.266, G.267, K.268, L.269, Q.372, R.384, L.388, R.389, R.390, C.391, K.435 Chain B: G.4, C.5, T.6, C.7, A.8, C.9, A.10, C.11, T.12 Ligands: 0KX.2, MG.4, 9RD.8 Protein-ligand interaction information (PLIP) not available

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.20, M.21, D.22, C.23, F.24, F.25, I.55, A.56, Y.59, R.62, R.68, I.121, D.122, K.238 Chain B: G.4 Ligands: DT-DA-DG-DT-DG-DT-DG-DA-DG.1, MG.3, MG.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.25 Hydrogen bonds: A:D.20, A:D.22, A:D.22, A:C.23, A:F.24, A:F.25, A:R.62, A:R.68 Water bridges: A:D.20, A:D.20 Salt bridges: A:R.62, A:K.238

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: D.20, M.21, D.122, K.238 Ligands: 0KX.2, MG.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.20, A:M.21, A:D.122 MG.4: 7 residues within 4Å: Chain A: D.20, S.120, D.122, E.123 Ligands: DT-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.20, A:D.122, A:E.123, H2O.3

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: P.251, F.254, S.255, G.283, E.284, T.286 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.284 GOL.6: 3 residues within 4Å: Chain A: Q.27, R.37, G.216 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.27 Water bridges: A:Q.218 GOL.7: 3 residues within 4Å: Chain A: N.33, P.34, H.35 No protein-ligand interaction detected (PLIP)

1 x 9RD: (cyclohex-1-ene-1,2-diamine)platinum(2+)(Non-functional Binders)

9RD.8: 5 residues within 4Å: Chain B: G.3, G.4, C.5 Ligands: DT-DA-DG-DT-DG-DT-DG-DA-DG.1, DT-DA-DG-DT-DG-DT-DG-DA-DG.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ouzon-Shubeita, H. et al., Structural basis for the bypass of the major oxaliplatin-DNA adducts by human DNA polymerase eta. Biochem. J. (2019)

Release Date

2019-02-13

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase eta