SMTL ID : 8rvn.1

Nipah virus (NiV) fusion protein in complex with neutralizing Fab92

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-mer

Ligands

12 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 4 residues within 4Å: Chain A: N.42, N.155, V.159 Chain C: Q.169 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:Q.169, A:N.42 Hydrophobic interactions: A:V.159 NAG.2: 2 residues within 4Å: Chain A: E.70, N.74 No protein-ligand interaction detected (PLIP) NAG.3: 4 residues within 4Å: Chain A: N.389, G.405, K.406 Chain C: V.93 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.93 NAG.4: 3 residues within 4Å: Chain A: N.439 Chain C: Q.434, M.438 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.439 NAG.5: 2 residues within 4Å: Chain B: N.42, N.130 No protein-ligand interaction detected (PLIP) NAG.6: 2 residues within 4Å: Chain B: E.70, N.74 No protein-ligand interaction detected (PLIP) NAG.7: 2 residues within 4Å: Chain B: N.389, K.406 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.389 NAG.8: 3 residues within 4Å: Chain A: Q.434 Chain B: N.439, Q.443 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.443 Hydrophobic interactions: A:Q.434 NAG.9: 2 residues within 4Å: Chain B: Q.169 Chain C: N.42 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.42, B:Q.169 NAG.10: 3 residues within 4Å: Chain C: E.70, I.71, N.74 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.71 Hydrogen bonds: C:E.70, C:E.70, C:N.74 NAG.11: 2 residues within 4Å: Chain C: N.389, G.405 No protein-ligand interaction detected (PLIP) NAG.12: 3 residues within 4Å: Chain B: Q.434 Chain C: N.439, Q.443 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.439

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Avanzato, V.A. et al., A monoclonal antibody targeting the Nipah virus fusion glycoprotein apex imparts protection from disease. J.Virol. (2024)

Release Date

2024-09-04

Peptides

Fusion glycoprotein F0: ABC
Fab92 heavy chain: D
Fab92 light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
B

C
C

D
H

E
L

Fusion glycoprotein F0

Fab92 heavy chain

Fab92 light chain