SMTL ID : 7uob.1

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

Coordinates

PDB Format

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: 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

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.618, D.760, D.761 Ligands: GTP.6, L2B.8 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.618, A:D.760, A:D.761, H2O.11 MG.4: 4 residues within 4Å: Chain A: D.618, Y.619, D.760 Ligands: GTP.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.618, A:Y.619, A:D.760 MG.5: 4 residues within 4Å: Chain A: D.208, N.209, D.218 Ligands: GTP.7 No protein-ligand interaction detected (PLIP)

2 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.6: 21 residues within 4Å: Chain A: K.545, R.553, R.555, V.557, D.618, Y.619, P.620, K.621, C.622, D.623, S.682, G.683, T.687, N.691, D.760, K.798 Chain F: C.19, A.20 Ligands: MG.3, MG.4, L2B.8 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:K.621, A:C.622, A:D.623, A:S.682, A:S.682, A:N.691, A:S.759 Water bridges: A:K.545 Salt bridges: A:R.553, A:R.555, A:R.555, A:K.798 GTP.7: 20 residues within 4Å: Chain A: V.31, R.33, F.35, K.50, N.52, R.55, Y.69, V.71, K.73, H.75, R.116, L.119, T.120, K.121, T.123, D.208, N.209, Y.217, D.218 Ligands: MG.5 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:R.33, A:N.52, A:R.55, A:N.209, A:Y.217, A:Y.217, A:Y.217 Water bridges: A:T.123, A:T.123 Salt bridges: A:K.50, A:K.50, A:K.73, A:K.73, A:K.73, A:H.75, A:R.116 pi-Cation interactions: A:R.33, A:R.33

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

L2B.8: 9 residues within 4Å: Chain A: S.759, D.760, D.761, C.813, S.814 Chain E: A.35 Chain F: A.20 Ligands: MG.3, GTP.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.759, A:D.760, A:D.760, A:S.814 Water bridges: A:C.813

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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