SMTL ID : 6d0z.1

Polymerase Eta cytarabine (AraC) extension ternary complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x DA- DG- DC- DA- DC- DT- DG- CAR: DNA/RNA (5'-D(*AP*GP*CP*AP*CP*TP*G)-R(P*(CAR))-3')(Non-covalent)

DA-DG-DC-DA-DC-DT-DG-CAR.1: 31 residues within 4Å: Chain A: R.64, S.116, I.117, D.118, E.119, K.227, I.258, R.259, S.260, L.261, G.262, G.263, K.264, L.265, Q.368, R.380, L.384, R.385, R.386, C.387 Chain B: T.4, G.5, C.6, A.7, G.8, T.9, G.10, C.11, T.12 Ligands: MG.3, DZ4.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.116, A:D.118, A:E.119 Water bridges: A:I.117, A:K.227, A:R.259 Salt bridges: A:K.227

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: D.16, M.17, F.20, D.118, K.234 Ligands: MG.3, DZ4.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.16, A:M.17, A:D.118 MG.3: 7 residues within 4Å: Chain A: D.16, S.116, D.118, E.119 Ligands: DA-DG-DC-DA-DC-DT-DG-CAR.1, MG.2, DZ4.4 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 DZ4: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine(Non-covalent)

DZ4.4: 22 residues within 4Å: Chain A: D.16, M.17, D.18, C.19, F.20, F.21, Q.41, I.51, A.52, V.53, Y.55, R.58, R.64, I.117, D.118, K.234 Chain B: T.3, T.4, G.5 Ligands: DA-DG-DC-DA-DC-DT-DG-CAR.1, MG.2, MG.3 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.21, A:A.52 Hydrogen bonds: A:M.17, A:C.19, A:F.20, A:F.21, A:Y.55, A:R.64 Water bridges: A:Q.41, A:I.51, A:Y.55, A:R.58, A:R.58, A:R.58, A:R.58, A:R.58 Salt bridges: A:R.58, A:K.234

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: G.274, I.275, E.276, Y.277, E.280 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.274, A:E.280 Water bridges: A:E.276, A:E.280 GOL.6: 7 residues within 4Å: Chain A: P.247, Q.248, F.250, S.251, G.279, E.280, T.282 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.247 Water bridges: A:T.282

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rechkoblit, O. et al., Structural basis for polymerase eta-promoted resistance to the anticancer nucleoside analog cytarabine. Sci Rep (2018)

Release Date

2018-09-05

Peptides

DNA polymerase eta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase eta

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