SMTL ID : 7doi.1

Structure of COVID-19 RNA-dependent RNA polymerase bound to penciclovir.

Coordinates

PDB Format Compare

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.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: 4 residues within 4Å: Chain A: C.488, H.643, C.646, C.647 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.488, A:C.646, A:C.647

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

POP.3: 7 residues within 4Å: Chain A: K.552, R.554, Y.620, P.621, K.622 Ligands: MG.4, HCU.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.622 Salt bridges: A:K.552, A:R.554, A:R.554, A:K.622 POP.8: 8 residues within 4Å: Chain A: K.51, N.53, K.74, R.117, N.210, D.219 Ligands: MG.6, MG.7 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.53, A:N.210 Salt bridges: A:K.51, A:K.51, A:K.74, A:K.74, A:R.117

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: Y.620, D.761 Ligands: POP.3, HCU.9 No protein-ligand interaction detected (PLIP) MG.5: 5 residues within 4Å: Chain A: D.762, E.812, C.814, S.815 Chain D: U.12 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.762 MG.6: 2 residues within 4Å: Chain A: D.219 Ligands: POP.8 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.219 MG.7: 4 residues within 4Å: Chain A: D.209, N.210, D.219 Ligands: POP.8 No protein-ligand interaction detected (PLIP)

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

HCU.9: 11 residues within 4Å: Chain A: K.546, D.624, S.683, T.688, N.692, D.761 Chain D: U.12 Chain E: U.3, A.4 Ligands: POP.3, MG.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.546, A:D.624

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: A
Non-structural protein 8: BF
Non-structural protein 7: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

F
G

C
C

RNA-directed RNA polymerase

Non-structural protein 8

Non-structural protein 7

Related Entries With Identical Sequence