SMTL ID : 8gw1.1

A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-1-2-1-mer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.295, C.301, C.306, C.310 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.295, A:C.301, A:C.306, A:C.310 ZN.2: 5 residues within 4Å: Chain A: C.487, F.571, H.642, C.645, C.646 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.487, A:H.642, A:C.645, A:C.646 ZN.5: 5 residues within 4Å: Chain G: C.16, C.19, H.33, H.39, A.110 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.16, G:C.19, G:H.33, G:H.39 ZN.6: 4 residues within 4Å: Chain G: C.5, C.8, C.26, C.29 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.5, G:C.8, G:C.26, G:C.29 ZN.7: 4 residues within 4Å: Chain G: C.50, C.55, C.72, H.75 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:C.50, G:C.55, G:C.72, G:H.75, G:H.75 ZN.8: 5 residues within 4Å: Chain H: C.16, C.19, H.33, H.39, A.110 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.16, H:C.19, H:H.33, H:H.39 ZN.9: 4 residues within 4Å: Chain H: C.5, C.8, C.26, C.29 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.5, H:C.8, H:C.26, H:C.29 ZN.10: 4 residues within 4Å: Chain H: C.50, C.55, C.72, H.75 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:C.50, H:C.55, H:C.72, H:H.75, H:H.75

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

MN.3: 4 residues within 4Å: Chain A: D.218, D.221 Ligands: MN.4, U5P.11 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.218, A:D.218, U5P.11 MN.4: 5 residues within 4Å: Chain A: D.208, N.209, D.218 Ligands: MN.3, U5P.11 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.218

1 x U5P: URIDINE-5'-MONOPHOSPHATE(Covalent)

U5P.11: 11 residues within 4Å: Chain A: F.35, I.37, N.39, V.42, L.49, K.50, D.208, D.218 Chain I: N.1 Ligands: MN.3, MN.4 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain I Hydrophobic interactions: A:I.37, I:N.1 Hydrogen bonds: A:N.39, A:L.49, I:N.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, L. et al., A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analog inhibitors. Cell (2022)

Release Date

2023-10-25

Peptides

Replicase polyprotein 1ab: A
Non-structural protein 8: BD
Non-structural protein 7: C
Helicase: GH
Non-structural protein 9: I

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

C
C

G
E

H
F

I
G

Replicase polyprotein 1ab

Non-structural protein 8

Non-structural protein 7

Helicase

Non-structural protein 9

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