SMTL ID : 7aap.1

Nsp7-Nsp8-Nsp12 SARS-CoV2 RNA-dependent RNA polymerase in complex with template:primer dsRNA and favipiravir-RTP

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: 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

3 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 4 residues within 4Å: Chain A: Y.619, D.760 Ligands: MG.6, GE6.7 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain A: N.209, D.218 Ligands: POP.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.218 MG.6: 3 residues within 4Å: Chain E: U.24 Ligands: MG.3, GE6.7 No protein-ligand interaction detected (PLIP)

1 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.5: 8 residues within 4Å: Chain A: K.50, N.52, K.73, R.116, N.209, Y.217, D.218 Ligands: MG.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.52, A:D.218, A:D.218 Salt bridges: A:K.50, A:K.50, A:K.73, A:K.73, A:R.116

1 x GE6: [[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonyl-5-fluoranyl-2-oxidanylidene-pyrazin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate(Non-covalent)

GE6.7: 12 residues within 4Å: Chain A: K.545, D.623, S.682, T.687, N.691, D.760, S.814 Chain E: U.24 Chain F: C.6, A.7 Ligands: MG.3, MG.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.623, A:D.623, A:S.682, A:N.691

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Naydenova, K. et al., Structure of the SARS-CoV-2 RNA-dependent RNA polymerase in the presence of favipiravir-RTP. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2020-09-23

Peptides

Non-structural protein 12: 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

Non-structural protein 12

Non-structural protein 8

Non-structural protein 7

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