SMTL ID : 7d4f.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain D: H.296, C.302, C.307, C.311 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.296, D:C.302, D:C.307, D:C.311 ZN.2: 4 residues within 4Å: Chain D: C.488, H.643, C.646, C.647 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.488, D:C.646, D:C.647

2 x H3U: 8-(3-(3-aminobenzamido)-4-methylbenzamido)naphthalene-1,3,5-trisulfonic acid(Non-covalent)

H3U.3: 12 residues within 4Å: Chain D: N.497, N.498, K.501, R.570, Q.574, L.577, K.578, A.581, G.591, A.686, Y.690, L.759 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:K.578, D:A.686, D:L.759 Hydrogen bonds: D:N.498, D:N.498, D:N.498, D:R.570, D:Q.574, D:K.578, D:G.591 Salt bridges: D:K.501, D:R.570, D:K.578 pi-Cation interactions: D:K.578 H3U.4: 12 residues within 4Å: Chain D: H.440, I.549, S.550, A.551, K.552, R.554, R.556, R.837, A.841, S.862, L.863, D.866 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:R.837, D:L.863 Hydrogen bonds: D:A.551, D:K.552, D:R.556, D:R.556, D:R.837, D:R.837, D:D.866 Salt bridges: D:K.552, D:R.554, D:R.556 pi-Cation interactions: D:R.556, D:R.556, D:R.837

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yin, W. et al., Structural basis for inhibition of the SARS-CoV-2 RNA polymerase by suramin. Nat.Struct.Mol.Biol. (2021)

Release Date

2020-11-11

Peptides

Non-structural protein 8: AC
Non-structural protein 7: B
RNA-directed RNA polymerase: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

C
G

B
C

D
A

Non-structural protein 8

Non-structural protein 7

RNA-directed RNA polymerase

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