SMTL ID : 7dfh.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-1-mer

Ligands

1 x G- C- U- A- U- G- U- G: RNA (5'-R(P*GP*CP*UP*AP*UP*GP*UP*G*(LIG))-3')(Non-covalent)

G-C-U-A-U-G-U-G.1: 22 residues within 4Å: Chain A: R.514, S.760, D.761, C.814, S.815, R.837, A.841, D.846, K.850, L.855, E.858, R.859, D.866 Chain E: C.5, A.6, C.7, A.8, U.9, A.10, G.11, C.12 Ligands: RVP.9 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:N.497, A:N.497, A:S.502, A:S.502, A:N.544, A:R.570, A:G.591, A:S.593, A:S.593, A:Y.596, A:G.684, A:A.686, A:Y.690 Salt bridges: A:K.501, A:K.512, A:R.570, A:K.578, A:E.858

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 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.3: 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

3 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: K.51, N.210, D.219 Ligands: POP.7 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain A: Y.620, D.761 Ligands: POP.8, RVP.9 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.761, RVP.9 MG.6: 2 residues within 4Å: Chain A: D.762 Ligands: RVP.9 No protein-ligand interaction detected (PLIP)

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

POP.7: 7 residues within 4Å: Chain A: K.51, K.74, R.117, N.210, Y.218, D.219 Ligands: MG.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.53 Salt bridges: A:K.51, A:K.51, A:K.74, A:K.74, A:R.117 POP.8: 5 residues within 4Å: Chain A: Y.620, K.622, C.623 Ligands: MG.5, RVP.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.622, A:C.623

1 x RVP: RIBAVIRIN MONOPHOSPHATE(Non-covalent)

RVP.9: 14 residues within 4Å: Chain A: K.546, R.556, V.558, C.623, D.624, T.681, S.683, N.692, D.761 Chain E: C.4 Ligands: G-C-U-A-U-G-U-G.1, MG.5, MG.6, POP.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.556, A:D.624, A:D.624, A:S.683, 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 repurpose and design of nucleotide drugs for treating COVID-19. To Be Published

Release Date

2021-11-17

Peptides

RNA-directed RNA polymeras: A
Non-structural protein 8: BD
Non-structural protein 7: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
G

C
C

RNA-directed RNA polymeras

Non-structural protein 8

Non-structural protein 7

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