SMTL ID : 7dfg.1

Structure of COVID-19 RNA-dependent RNA polymerase bound to favipiravir

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-1-mer

Ligands

1 x 1RP: 6-fluoro-3-oxo-4-(5-O-phosphono-beta-D-ribofuranosyl)-3,4-dihydropyrazine-2-carboxamide(Non-covalent)

1RP.1: 11 residues within 4Å: Chain A: U.12 Chain B: U.4, A.5 Chain C: K.546, D.624, T.681, S.683, T.688, N.692, D.761 Ligands: MG.6 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.546, C:K.546, C:D.624, C:T.681, C:T.681

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain C: H.296, C.302, C.307, C.311 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.296, C:C.302, C:C.307, C:C.311 ZN.3: 4 residues within 4Å: Chain C: C.488, H.643, C.646, C.647 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.488, C:C.646, C:C.647

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

POP.4: 5 residues within 4Å: Chain C: K.552, R.554, P.621, K.622 Ligands: MG.5 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:K.622 Water bridges: C:R.556 Salt bridges: C:K.552, C:K.552, C:R.554, C:K.622 POP.7: 9 residues within 4Å: Chain C: K.51, N.53, K.74, R.117, N.210, Y.218, D.219 Ligands: MG.8, MG.9 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.53 Salt bridges: C:K.51, C:K.51, C:K.74, C:K.74, C:R.117

4 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain C: D.619, Y.620 Ligands: POP.4 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: POP.4 MG.6: 4 residues within 4Å: Chain A: U.12 Chain C: D.761, D.762 Ligands: 1RP.1 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.761, C:D.762 MG.8: 3 residues within 4Å: Chain C: N.210, D.219 Ligands: POP.7 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.219 MG.9: 2 residues within 4Å: Chain C: D.219 Ligands: POP.7 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.219, C:D.219

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yin, W. et al., Structural basis for repurpose and design of nucleotide drugs for treating COVID-19. To Be Published

Release Date

2021-11-17

Peptides

RNA-directed RNA polymerase: C
Non-structural protein 8: DF
Non-structural protein 7: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

D
B

F
G

E
C

RNA-directed RNA polymerase

Non-structural protein 8

Non-structural protein 7

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