SMTL ID : 8xpo.1

Cryo-EM structure of Lassa virus RdRP elongation complex with the NTP form of compound HNC-1664 bound in the active site

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

1 x G- G- A- C- U- C- U- U- C: RNA (9-MER)(Non-covalent)

G-G-A-C-U-C-U-U-C.1: 32 residues within 4Å: Chain A: K.714, L.822, S.826, N.827, H.1301, S.1332, S.1333, D.1334, K.1387, S.1388, K.1402, A.1406, I.1411, Q.1418, T.1422, I.1426, Q.1429, K.1590, L.1602, A.1606, K.1609 Chain C: G.22, A.23, A.24, G.25, A.26, G.27, U.28, C.29, C.30, A.31 Ligands: 01.2 Protein-ligand interaction information (PLIP) not available

1 x 01: [[(2~{R},3~{R},4~{S},5~{R})-4-fluoranyl-5-(5-iodanyl-4-methyl-pyrrolo[2,3-d]pyrimidin-7-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate

01.2: 13 residues within 4Å: Chain A: K.662, K.1127, Q.1129, R.1134, S.1195, K.1196, Q.1297, G.1298, S.1374, K.1376 Chain C: U.21, G.22 Ligands: G-G-A-C-U-C-U-U-C.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Q.1129, A:R.1134, A:K.1196, A:S.1374 Salt bridges: A:K.662, A:K.729, A:R.1134, A:K.1376, A:K.1376, A:K.1376 pi-Cation interactions: A:R.1134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jia, X. et al., An adenosine analog shows high antiviral potency against coronavirus and arenavirus mainly through an unusual base pairing mode. Nat Commun (2024)

Release Date

2024-12-04

Peptides

RNA-directed RNA polymerase L: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

RNA-directed RNA polymerase L