SMTL ID : 8sqk.1

SARS-CoV-2 replication-transcription complex bound to RNA-nsp9 and GDP-betaS, as a pre-catalytic deRNAylation/mRNA capping intermediate

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-1-1-mer

Ligands

2 x VSN: 5'-O-[(R)-hydroxy(thiophosphonooxy)phosphoryl]guanosine(Non-covalent)

VSN.1: 14 residues within 4Å: Chain A: K.545, R.555, V.557, C.622, D.623, T.680, S.682, T.687, N.691, S.759, D.760 Chain F: G.32 Chain G: U.3, C.4 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:K.545, A:R.555, A:C.622, A:D.623, A:D.623, A:S.682, A:N.691, A:N.691 Water bridges: A:Y.619, A:S.759, A:D.760 VSN.2: 20 residues within 4Å: Chain A: V.31, R.33, F.35, K.50, C.53, R.55, Y.69, V.71, K.73, R.116, L.119, T.120, K.121, T.123, D.208, D.211, Y.217, D.218 Chain H: A.1 Ligands: MG.5 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:R.33, A:R.33, A:K.50, A:R.55, A:K.73, A:T.120, A:D.208, A:D.208, A:Y.217, A:Y.217 Water bridges: A:A.34, A:T.123 Salt bridges: A:K.73, A:R.116 pi-Cation interactions: A:R.33

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 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.4: 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

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 5 residues within 4Å: Chain A: D.208, N.209, D.218 Chain H: A.1 Ligands: VSN.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.218

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Small, G.I. et al., Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN domain. Mol.Cell (2023)

Release Date

2023-11-22

Peptides

RNA-directed RNA polymerase nsp12: A
Non-structural protein 8: BD
Non-structural protein 7: C
Non-structural protein 9: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

C
C

E
G

RNA-directed RNA polymerase nsp12

Non-structural protein 8

Non-structural protein 7

Non-structural protein 9

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