SMTL ID : 9vck.1

Cryo-EM structure of SARS-CoV-2 nsp10/nsp14:RNA:SMP 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, K.124, C.128, C.130 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.128, A:C.130 ZN.5: 5 residues within 4Å: Chain B: C.206, L.208, C.209, C.225, H.228 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.206, B:C.209, B:C.225, B:H.228 ZN.6: 4 residues within 4Å: Chain B: H.256, C.260, H.263, C.278 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.256, B:H.263, B:C.278 ZN.7: 4 residues within 4Å: Chain B: C.451, C.476, C.483, H.486 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.451, B:C.483, B:H.486

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain B: D.89, E.91, D.272 Ligands: K5X.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.89, B:D.272 CA.4: 4 residues within 4Å: Chain B: D.89, A.186, E.190 Ligands: K5X.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.89, B:E.190

1 x K5X: [(2~{R},3~{R},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate

K5X.8: 10 residues within 4Å: Chain B: D.89, V.90, E.91, G.92, H.94, P.140 Chain C: C.26 Chain D: G.3 Ligands: CA.3, CA.4 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.140 Hydrogen bonds: B:E.91, B:G.92

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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