SMTL ID : 9cgv.1

SARS-CoV-2 nsp12 NiRAN domain bound to a covalent inhibitor SW090466-1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.311, C.317, C.322, C.326 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.311, A:C.317, A:C.322, A:C.326 ZN.2: 7 residues within 4Å: Chain A: G.502, C.503, K.548, F.587, H.658, C.661, C.662 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.503, A:H.658, A:C.661, A:C.662

1 x 01: methyl (8S)-7-hydroxy-5-methylpyrazolo[1,5-a]pyrimidine-3-carboxylate

01.3: 14 residues within 4Å: Chain A: K.66, T.67, C.69, R.71, V.87, K.89, R.132, L.135, T.136, K.137, Y.138, T.139, D.227, Y.233 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.87 Hydrogen bonds: A:K.66, A:R.132 Water bridges: A:V.87, A:H.91, A:R.132 Salt bridges: A:K.66, A:R.71

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.4: 2 residues within 4Å: Chain A: N.225, D.234 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hernandez, G. et al., Covalent inhibition of the SARS-CoV-2 NiRAN domain via an active-site cysteine. J.Biol.Chem. (2025)

Release Date

2025-03-12

Peptides

RNA-directed RNA polymerase nsp12: A
Non-structural protein 8: BD
Non-structural protein 7: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

C
C

RNA-directed RNA polymerase nsp12

Non-structural protein 8

Non-structural protein 7

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