SMTL ID : 9dj8.1

RNA-nsp9 bound to the NiRAN domain of the E-RTC with an empty G-pocket

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

2 x ZN: ZINC ION

ZN.1: 4 residues within 4Å: Chain A: H.295, C.301, C.306, C.310 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.295, A:C.301, A:C.306, A:C.310 ZN.2: 6 residues within 4Å: Chain A: C.487, K.532, F.571, H.642, C.645, C.646 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.487, A:H.642, A:C.645, A:C.646

1 x AMP: ADENOSINE MONOPHOSPHATE

AMP.3: 13 residues within 4Å: Chain A: F.35, I.37, N.39, K.41, V.42, F.48, L.49, K.50, T.51, D.208, D.218, N.713 Chain B: N.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.39, A:K.41, A:L.49, A:K.50, A:N.713, A:N.713 pi-Stacking: A:F.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Small, G.I. et al., The mechanism for GTP-mediated RNA capping by the SARS-CoV-2 NiRAN domain remains unresolved. Cell (2025)

Release Date

2025-03-19

Peptides

RNA-directed RNA polymerase: A
Non-structural protein 9: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
G

RNA-directed RNA polymerase

Non-structural protein 9

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