SMTL ID : 7bv2.1

The nsp12-nsp7-nsp8 complex bound to the template-primer RNA and triphosphate form of Remdesivir(RTP)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.296, C.302, C.307, C.311 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.296, A:C.302, A:C.307, A:C.311 ZN.2: 5 residues within 4Å: Chain A: C.488, F.572, H.643, C.646, C.647 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.488, A:H.643, A:C.646, A:C.647

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

POP.3: 5 residues within 4Å: Chain A: R.554, C.623, D.624 Ligands: MG.4, F86.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.624, A:D.624 Salt bridges: A:R.554

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: Y.620, D.761 Ligands: POP.3, F86.6 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: POP.3 MG.5: 3 residues within 4Å: Chain A: D.762 Chain D: U.20 Ligands: F86.6 No protein-ligand interaction detected (PLIP)

1 x F86: [(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]methyl dihydrogen phosphate(Non-covalent)

F86.6: 13 residues within 4Å: Chain A: K.546, R.556, D.624, S.683, T.688, N.692, D.761 Chain D: U.20 Chain E: U.10, A.11 Ligands: POP.3, MG.4, MG.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.556, A:R.556, A:N.692 pi-Cation interactions: A:R.556

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yin, W. et al., Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir. Science (2020)

Release Date

2020-04-22

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

RNA-directed RNA polymerase

Non-structural protein 8

Non-structural protein 7

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