SMTL ID : 5rmj.1 (1 other biounit)

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z68299550

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x JOV: 3-chloro-N-(1-hydroxy-2-methylpropan-2-yl)benzamide(Non-covalent)

JOV.1: 10 residues within 4Å: Chain A: F.472, M.474, V.495, E.498, F.499, R.502, N.503, L.590, E.591, P.593 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.499, A:L.590, A:P.593 Hydrogen bonds: A:N.503 pi-Cation interactions: A:R.502 Halogen bonds: A:V.495

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.16, 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.3: 5 residues within 4Å: Chain A: C.5, C.8, S.10, C.26, C.29 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.5, A:C.26, A:C.29 ZN.4: 5 residues within 4Å: Chain A: C.50, A.52, 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

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

PO4.5: 8 residues within 4Å: Chain A: P.283, G.285, T.286, G.287, K.288, S.289, R.443 Ligands: PO4.6 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.285, A:T.286, A:T.286, A:G.287, A:K.288, A:S.289, A:R.443 Salt bridges: A:K.288 PO4.6: 9 residues within 4Å: Chain A: P.283, P.284, G.285, K.288, Q.404, R.443, G.538, R.567 Ligands: PO4.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.285, A:Q.404, A:G.538 Water bridges: A:Q.404 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
B

Helicase

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