SMTL ID : 8gwb.1

SARS-CoV-2 E-RTC complex with RNA-nsp9

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x A- U: RNA (5'-R(P*AP*U)-3')(Non-covalent)

A-U.1: 12 residues within 4Å: Chain A: I.37, N.39, L.49, K.50, T.51, N.52, D.208, D.218, N.713 Chain G: N.5 Ligands: MN.4, MN.5 Protein-ligand interaction information (PLIP) not available

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 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.3: 6 residues within 4Å: Chain A: C.487, K.532, 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.6: 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.7: 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.8: 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.9: 5 residues within 4Å: Chain F: C.16, A.18, C.19, H.33, H.39 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.16, F:C.19, F:H.33, F:H.39 ZN.10: 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.11: 6 residues within 4Å: Chain F: C.50, C.55, V.57, C.72, S.74, H.75 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.50, F:C.55, F:C.72, F:H.75

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

MN.4: 4 residues within 4Å: Chain A: D.218, D.221 Ligands: A-U.1, MN.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.218, A:D.218, H2O.1, H2O.1 MN.5: 5 residues within 4Å: Chain A: D.208, N.209, D.218 Ligands: A-U.1, MN.4 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.218, H2O.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

2022-12-07

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
F

F
E

G
G

RNA-directed RNA polymerase

Non-structural protein 8

Non-structural protein 7

Helicase

Non-structural protein 9

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