SMTL ID : 8gwg.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: 4 residues within 4Å: Chain A: C.487, 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.4: 5 residues within 4Å: Chain G: C.16, A.18, C.19, H.33, H.39 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.16, G:C.19, G:H.33, G:H.39 ZN.5: 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.6: 4 residues within 4Å: Chain G: C.50, C.55, C.72, H.75 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.50, G:C.55, G:C.72, G:H.75 ZN.7: 4 residues within 4Å: Chain H: C.16, C.19, H.33, H.39 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.16, H:C.19, H:H.33, H:H.39 ZN.8: 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.9: 5 residues within 4Å: Chain H: C.50, A.52, C.55, C.72, H.75 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.50, H:C.55, H:C.72, H:H.75

1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.3: 15 residues within 4Å: Chain A: F.35, K.50, R.55, V.71, K.73, R.116, T.120, K.121, Y.122, T.123, D.208, N.209, Y.217, D.218 Chain I: N.5 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain I Hydrogen bonds: A:R.55, A:T.120, A:T.120, A:D.208, A:D.208, A:N.209, A:D.218, A:D.218, I:N.5 Salt bridges: A:K.50, A:K.50, A:K.50, A:K.73, A:K.73, A:H.75, A:R.116 pi-Cation interactions: A:R.33, A:R.33

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

2022-12-14

Peptides

RNA-directed RNA polymerase: 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
F

H
E

I
G

RNA-directed RNA polymerase

Non-structural protein 8

Non-structural protein 7

Helicase

Non-structural protein 9

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