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

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z2467208649

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

monomer

Ligands

2 x VWJ: N-(propan-2-yl)-1H-benzimidazol-2-amine(Non-covalent)

VWJ.1: 5 residues within 4Å: Chain A: E.261, G.287, H.290, Y.324, R.442 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:H.290 Hydrogen bonds: A:Y.324, A:Y.324 Water bridges: A:H.290 pi-Stacking: A:H.290, A:H.290 VWJ.2: 5 residues within 4Å: Chain A: E.365, T.366, A.389, R.390, R.392 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.365, A:E.365

3 x ZN: ZINC ION(Non-covalent)

ZN.3: 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.4: 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.5: 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)

PO4.6: 8 residues within 4Å: Chain A: P.283, G.285, T.286, G.287, K.288, S.289, R.443 Ligands: PO4.7 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.285, A:T.286, A:G.287, A:K.288, A:S.289, A:R.443 Water bridges: A:S.289 Salt bridges: A:K.288 PO4.7: 9 residues within 4Å: Chain A: P.284, G.285, K.288, Q.404, R.443, Q.537, G.538, R.567 Ligands: PO4.6 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.285, 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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