SMTL ID : 9vcl.1

Cryo-EM structure of SARS-CoV-2 nsp10/nsp14:RNA:ATMP complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

5 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.74, C.77, H.83, C.90 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.74, A:C.77, A:H.83, A:C.90 ZN.2: 4 residues within 4Å: Chain A: C.117, C.120, C.128, C.130 No protein-ligand interaction detected (PLIP) ZN.5: 5 residues within 4Å: Chain B: C.207, C.210, R.212, C.226, H.229 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.207, B:C.210, B:C.226, B:H.229 ZN.6: 4 residues within 4Å: Chain B: H.257, C.261, H.264, C.279 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.257, B:C.261, B:H.264, B:C.279 ZN.7: 4 residues within 4Å: Chain B: C.452, C.477, C.484, H.487 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.452, B:C.484, B:H.487

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain B: D.90, E.92, D.273 Ligands: EIF.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.90, B:E.92, B:D.273 CA.4: 5 residues within 4Å: Chain B: D.90, A.187, E.191 Chain C: C.26 Ligands: EIF.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.191, B:E.191

1 x EIF: [(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate(Non-covalent)

EIF.8: 11 residues within 4Å: Chain B: E.92, G.93, H.95, P.141, P.142, Q.145, F.146 Chain C: C.26 Chain D: G.3 Ligands: CA.3, CA.4 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:P.141, B:F.146 Hydrogen bonds: B:E.92, B:G.93, B:H.95, B:Q.145 pi-Stacking: B:F.146, B:F.146

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J. et al., Structural Basis and Rational Design of Nucleotide Analogue Inhibitor Evading the SARS-CoV-2 Proofreading Enzyme. J.Am.Chem.Soc. (2025)

Release Date

2025-07-16

Peptides

Non-structural protein 10: A
Guanine-N7 methyltransferase nsp14: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Non-structural protein 10

Guanine-N7 methyltransferase nsp14

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