SMTL ID : 9i1s.2 (1 other biounit)

Crystal structure of the SARS-CoV-2 helicase NSP13 in complex with myricetin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.18, C.21, H.35, H.41 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.18, A:C.21, A:H.35, A:H.41 ZN.2: 4 residues within 4Å: Chain A: C.7, C.10, C.28, C.31 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.7, A:C.10, A:C.28, A:C.31 ZN.3: 4 residues within 4Å: Chain A: C.52, C.57, C.74, H.77 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.52, A:C.57, A:C.74, A:H.77

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

PO4.4: 7 residues within 4Å: Chain A: P.285, G.287, T.288, G.289, K.290, R.445 Ligands: PO4.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.287, A:T.288, A:T.288, A:G.289, A:K.290 Water bridges: A:S.291, A:S.291 Salt bridges: A:K.290, A:R.445 PO4.5: 9 residues within 4Å: Chain A: P.286, G.287, K.290, Q.406, R.445, Q.539, G.540, R.569 Ligands: PO4.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.287, A:Q.406, A:G.540 Salt bridges: A:K.290, A:R.445, A:R.569

1 x MPO: 3[N-MORPHOLINO]PROPANE SULFONIC ACID(Non-covalent)

MPO.6: 7 residues within 4Å: Chain A: N.179, S.487, S.488, P.516, Y.517, N.518, H.556 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.179, A:N.518

1 x MYC: 3,5,7-TRIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)-4H-CHROMEN-4-ONE(Non-covalent)

MYC.7: 10 residues within 4Å: Chain A: S.238, A.239, P.240, V.243, K.278, N.390, L.393, R.394, A.395, Y.398 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.243 Hydrogen bonds: A:S.238, A:N.390, A:R.394, A:R.394, A:Y.398 pi-Cation interactions: A:R.394

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kloskowski, P. et al., Myricetin-bound crystal structure of the SARS-CoV-2 helicase NSP13 facilitates the discovery of novel natural inhibitors. Acta Crystallogr D Struct Biol (2025)

Release Date

2025-06-11

Peptides

Helicase nsp13: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Helicase nsp13

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