SMTL ID : 5rl7.2 (1 other biounit)

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z364321922

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

monomer

Ligands

1 x VVD: 5-(acetylamino)-2-fluorobenzoic acid(Non-covalent)

VVD.1: 8 residues within 4Å: Chain A: S.264, G.285, T.286, G.287, H.290, K.320, R.442 Ligands: PO4.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:H.290, A:R.442 Water bridges: A:G.287, A:H.290, A:Y.324 Salt bridges: A:H.290, A:K.320

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.50, C.55, C.72, H.75 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.50, A:C.55, A:C.72, A:H.75 ZN.3: 5 residues within 4Å: Chain A: C.16, A.18, C.19, H.33, H.39 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.16, A:C.19, A:H.33, A:H.39 ZN.4: 4 residues within 4Å: Chain A: C.5, C.8, C.26, C.29 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.5, A:C.8, A:C.26, A:C.29

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 9 residues within 4Å: Chain A: P.283, G.285, T.286, G.287, K.288, S.289, R.443 Ligands: VVD.1, PO4.6 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:P.283, A:G.285, A:T.286, A:G.287, A:K.288, A:S.289, A:R.443 Salt bridges: A:K.288 PO4.6: 8 residues within 4Å: Chain A: P.284, K.288, Q.404, R.443, Q.537, G.538, R.567 Ligands: PO4.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.404, A:Q.404, A:Q.404, A:G.538 Water bridges: A:R.443, A:G.538 Salt bridges: A:K.288, A:R.443, A:R.567

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Newman, J.A. et al., Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase. Nat Commun (2021)

Release Date

2020-09-30

Peptides

Helicase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Helicase

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