SMTL ID : 7nng.1 (1 other biounit)

Crystal structure of the SARS-CoV-2 helicase in complex with Z2327226104

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

monomer

Ligands

1 x UJK: 1-(2-methylphenyl)-1,2,3-triazole-4-carboxylic acid(Non-covalent)

UJK.1: 9 residues within 4Å: Chain A: G.285, T.286, G.287, H.290, K.320, K.323, Y.324, R.442 Ligands: PO4.5 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:H.290, A:R.442 Hydrogen bonds: A:Y.324 Water bridges: A:K.320, A:K.320 Salt bridges: A:H.290, A:K.320, A:K.323 pi-Stacking: A:H.290

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, L.7, C.8, 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: 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

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

PO4.5: 8 residues within 4Å: Chain A: P.283, T.286, G.287, K.288, S.289, R.443 Ligands: UJK.1, PO4.6 9 PLIP interactions: 9 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 Water bridges: A:H.290 Salt bridges: A:K.288 PO4.6: 8 residues within 4Å: Chain A: P.283, P.284, K.288, Q.404, R.443, G.538, R.567 Ligands: PO4.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.404, A:Q.404, 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

2021-04-07

Peptides

SARS-CoV-2 helicase NSP13: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

SARS-CoV-2 helicase NSP13

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