SMTL ID : 7uo4.1

SARS-CoV-2 replication-transcription complex bound to Remdesivir triphosphate, in a pre-catalytic state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-1-mer

Ligands

1 x NWX: [[(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]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate(Non-covalent)

NWX.1: 21 residues within 4Å: Chain A: K.545, K.551, R.555, V.557, D.618, Y.619, P.620, K.621, C.622, D.623, S.682, T.687, A.688, N.691, S.759, D.760, K.798 Chain E: G.35 Chain F: U.20, C.21 Ligands: MG.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Y.619, A:K.621, A:C.622, A:D.623, A:D.623, A:T.687, A:N.691, A:S.759, A:D.760 Salt bridges: A:K.551, A:K.798

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.618, Y.619, D.760 Ligands: NWX.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.618, A:Y.619, A:D.760

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.295, C.301, C.306, C.310 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.295, A:C.301, A:C.306, A:C.310, H2O.3 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malone, B.F. et al., Structural basis for substrate selection by the SARS-CoV-2 replicase. Nature (2023)

Release Date

2022-11-30

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

C
C

RNA-directed RNA polymerase

Non-structural protein 8

Non-structural protein 7

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