SMTL ID : 8gwk.1

SARS-CoV-2 RNA E-RTC complex with RMP-nsp9 and GMPPNP

Coordinates

PDB Format

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: 4 residues within 4Å: Chain G: C.16, 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.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 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.50, G:C.55, G:C.72, G:H.75 ZN.8: 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.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 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.50, H:C.55, H:C.72, H:H.75

1 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Covalent)

GNP.3: 19 residues within 4Å: Chain A: R.33, A.34, F.35, K.50, R.55, V.71, K.73, R.116, T.120, K.121, Y.122, T.123, D.208, N.209, D.211, Y.217, D.218 Ligands: MG.4, F86.11 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:R.33, A:R.55, A:T.120, A:T.123, A:D.208, A:D.208, A:N.209, A:N.209, A:Y.217, A:Y.217, A:D.218, A:G.220, A:D.221 Salt bridges: A:K.50, A:K.73, A:R.116 pi-Cation interactions: A:R.33

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: K.73 Ligands: GNP.3, F86.11 No protein-ligand interaction detected (PLIP)

1 x F86: [(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate(Covalent)

F86.11: 11 residues within 4Å: Chain A: F.35, I.37, N.39, K.41, V.42, F.48, L.49, N.713 Chain I: N.1 Ligands: GNP.3, MG.4 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain I Hydrophobic interactions: A:F.48 Hydrogen bonds: A:N.39, A:K.41, A:K.41, A:N.713, 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

2024-02-28

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
E

H
F

I
G

RNA-directed RNA polymerase

Non-structural protein 8

Non-structural protein 7

Helicase

Non-structural protein 9

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