SMTL ID : 8gwe.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

A-U-U-A.1: 18 residues within 4Å: Chain A: I.37, N.39, K.41, V.42, F.48, L.49, K.50, T.51, N.52, R.74, H.75, T.76, N.79, D.208, N.713 Chain G: N.1 Ligands: GNP.4, MG.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: 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.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: 5 residues within 4Å: Chain E: C.50, A.52, 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: 4 residues within 4Å: Chain F: C.50, 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.4: 17 residues within 4Å: Chain A: F.35, K.50, R.55, V.71, K.73, R.116, T.120, K.121, T.123, D.208, N.209, Y.217, D.218 Ligands: A-U-U-A.1, A-U-U-A.1, A-U-U-A.1, MG.5 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.55, A:K.73, A:T.120, A:T.123, A:D.208, A:Y.217, A:Y.217, A:D.218, A:D.218 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.5: 3 residues within 4Å: Chain A: K.50 Ligands: A-U-U-A.1, GNP.4 No protein-ligand interaction detected (PLIP)

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

2023-01-11

Peptides

RNA-directed RNA polymerase: A
Non-structural protein 8: BD
Replicase polyprotein 1a: C
Helicase nsp13: 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

Replicase polyprotein 1a

Helicase nsp13

Non-structural protein 9

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