SMTL ID : 7uoe.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-1-mer

Ligands

2 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

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.618, D.760, D.761 Ligands: CTP.5, L2B.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.618, A:D.760, A:D.761, H2O.7 MG.4: 4 residues within 4Å: Chain A: D.618, Y.619, D.760 Ligands: CTP.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.618, A:Y.619, A:D.760

1 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.5: 19 residues within 4Å: Chain A: K.551, R.553, R.555, D.618, Y.619, P.620, K.621, C.622, D.623, S.682, T.687, N.691, D.760, K.798 Chain F: G.19, A.20 Ligands: MG.3, MG.4, L2B.6 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:R.555, A:D.618, A:K.621, A:C.622, A:D.623, A:D.623, A:D.623, A:D.623, A:S.682, A:T.687, A:T.687, A:N.691, A:D.760 Water bridges: A:R.555, A:R.555, A:S.759 Salt bridges: A:K.551, A:R.553, A:R.555, A:R.555, A:K.798

1 x L2B: 3'-DEOXYURIDINE-5'-MONOPHOSPHATE(Non-covalent)

L2B.6: 10 residues within 4Å: Chain A: L.758, S.759, D.760, D.761, C.813, S.814 Chain E: A.35 Chain F: A.20 Ligands: MG.3, CTP.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.759, A:S.814 Water bridges: A:S.814

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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