SMTL ID : 5k8u.1

Crystal structure of ZIKV NS3 helicase in complex with ADP and Mn2+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 12 residues within 4Å: Chain A: H.32, P.33, G.34, A.35, G.36, K.37, T.38, R.39, N.167, N.254, R.299 Ligands: MN.2 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:G.34, A:G.34, A:A.35, A:G.36, A:K.37, A:T.38, A:R.39, A:R.39, A:N.167, A:R.299 Water bridges: A:R.39, A:R.39, A:R.39, A:N.254, A:N.254, A:R.296, A:R.299, A:R.299, A:R.299, A:R.299, A:R.299 Salt bridges: A:K.37, A:R.299, A:R.299 pi-Cation interactions: A:R.39, A:R.39

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 3 residues within 4Å: Chain A: T.38, E.123 Ligands: ADP.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.38, A:E.123, H2O.4, H2O.4, H2O.4 MN.3: 1 residues within 4Å: Chain A: H.32 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.32, H2O.2, H2O.10

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

EDO.4: 2 residues within 4Å: Chain A: V.175, W.188 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.307

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 3 residues within 4Å: Chain A: S.224, R.225, T.246 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, X. et al., Molecular mechanism of divalent-metal-induced activation of NS3 helicase and insights into Zika virus inhibitor design. Nucleic Acids Res. (2016)

Release Date

2016-11-09

Peptides

zika virus NS3 helicase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

zika virus NS3 helicase

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