SMTL ID : 9blf.1

SARS-CoV-2 core polymerase complex inhibited by araCTP

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.294, C.300, C.305, C.309 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.294, A:C.300, A:C.305, A:C.309 ZN.2: 5 residues within 4Å: Chain A: C.486, F.570, H.641, C.644, C.645 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.486, A:H.641, A:C.644, A:C.645

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.617, Y.618, C.621, D.759 Ligands: HF4.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:Y.618 MG.5: 4 residues within 4Å: Chain A: D.207, N.208, D.217 Ligands: HF4.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.217

2 x HF4: 4-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one(Non-covalent)

HF4.4: 22 residues within 4Å: Chain A: V.30, R.32, F.34, K.49, N.51, C.52, R.54, V.70, K.72, N.78, E.82, R.115, L.118, T.119, K.120, T.122, N.208, D.210, Y.216, D.217, G.219 Ligands: MG.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.70 Hydrogen bonds: A:N.51, A:E.82, A:R.115, A:T.119, A:Y.216 Salt bridges: A:K.72, A:K.72, A:K.72, A:R.115 HF4.6: 18 residues within 4Å: Chain A: K.544, K.550, R.552, R.554, V.556, D.617, Y.618, P.619, K.620, C.621, D.622, S.681, N.690, D.759, K.797 Chain E: C.30 Chain F: G.3 Ligands: MG.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.544, A:R.554, A:D.617, A:K.620, A:S.681, A:S.681, A:D.759 Salt bridges: A:R.552, A:R.554, A:K.797

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Anderson, T.K. et al., Structure of the SARS-CoV-2 core-RTC bound to RNA, araCMP, and araCTP. To Be Published

Release Date

2025-05-14

Peptides

RNA-directed RNA polymerase nsp12: A
Non-structural protein 8: BD
Non-structural protein 7: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

C
C

RNA-directed RNA polymerase nsp12

Non-structural protein 8

Non-structural protein 7