SMTL ID : 7dok.1

Structure of COVID-19 RNA-dependent RNA polymerase (extended conformation) bound to penciclovir

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-1-mer

Ligands

1 x HCU: [(2R)-4-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-(hydroxymethyl)butyl] dihydrogen phosphate(Non-covalent)

HCU.1: 11 residues within 4Å: Chain A: U.20 Chain B: U.4, A.5 Chain C: D.624, S.683, T.688, N.692, S.760, D.761 Ligands: MG.2, MG.6 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.546, C:K.546, C:D.624

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: U.20 Chain C: D.761 Ligands: HCU.1 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain C: Y.620, D.761 Ligands: HCU.1, POP.5 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain C: D.219 Ligands: MG.8, POP.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.219, C:D.219 MG.8: 5 residues within 4Å: Chain C: D.209, N.210, D.219 Ligands: MG.7, POP.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.219

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 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.4: 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.5: 6 residues within 4Å: Chain C: K.552, Y.620, P.621, K.622, K.799 Ligands: MG.6 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.622 Salt bridges: C:K.552, C:K.552, C:K.622, C:K.799 POP.9: 9 residues within 4Å: Chain C: K.51, N.53, K.74, R.117, N.210, Y.218, D.219 Ligands: MG.7, MG.8 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

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

2021-12-15

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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