SMTL ID : 8gwm.1

SARS-CoV-2 E-RTC bound with MMP-nsp9 and GMPPNP

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: 4 residues within 4Å: Chain E: C.16, C.19, H.33, H.39 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.16, E:C.19, E:H.33, E:H.39 ZN.5: 4 residues within 4Å: Chain E: C.5, C.8, C.26, C.29 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.5, E:C.8, E:C.26, E:C.29 ZN.6: 4 residues within 4Å: Chain E: C.50, C.55, C.72, H.75 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.50, E:C.55, E:C.72, E:H.75 ZN.7: 4 residues within 4Å: Chain F: C.16, C.19, H.33, H.39 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:C.16, F:C.19, F:H.33, F:H.39, F:H.39 ZN.8: 4 residues within 4Å: Chain F: C.5, C.8, C.26, C.29 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.5, F:C.8, F:C.26, F:C.29 ZN.9: 5 residues within 4Å: Chain F: C.50, A.52, C.55, C.72, H.75 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.50, F:C.55, F:C.72, F:H.75

1 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.3: 17 residues within 4Å: Chain A: R.33, F.35, K.50, R.55, Y.69, V.71, K.73, R.116, T.120, K.121, Y.122, T.123, D.208, N.209, Y.217, D.218 Ligands: 6GS.10 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:K.50, A:R.55, A:T.120, A:D.208, A:D.208, A:N.209, A:Y.217, A:Y.217, A:D.218 Water bridges: A:N.209, A:D.218 Salt bridges: A:K.50, A:R.116 pi-Cation interactions: A:R.33

1 x 6GS: 2'-deoxy-2'-fluoro-2'-methyluridine 5'-(trihydrogen diphosphate)(Covalent)

6GS.10: 11 residues within 4Å: Chain A: F.35, D.36, I.37, V.42, F.48, L.49, K.50, D.208, N.713 Chain G: N.1 Ligands: GNP.3 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain G Hydrophobic interactions: A:I.37 Hydrogen bonds: A:N.39, A:K.50, A:N.713 Water bridges: A:D.36, G:N.2, G:N.2 Halogen bonds: A:L.49

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

2024-02-28

Peptides

RNA-directed RNA polymerase: A
Non-structural protein 8: BD
Non-structural protein 7: C
Helicase: EF
Non-structural protein 9: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

C
C

E
E

F
F

G
G

RNA-directed RNA polymerase

Non-structural protein 8

Non-structural protein 7

Helicase

Non-structural protein 9

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