SMTL ID : 6t3f.1

Crystal structure Nipah virus fusion glycoprotein in complex with a neutralising Fab fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-3-3-3-mer

Ligands

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: N.442, Q.446 Chain D: Q.437 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain D: N.442, Q.446 Chain G: Q.437 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain A: Q.437 Chain G: N.442, Q.446 No protein-ligand interaction detected (PLIP)

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

NAG.2: 2 residues within 4Å: Chain A: E.73, N.77 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.73, A:N.77 NAG.3: 4 residues within 4Å: Chain A: N.45, N.133, N.158 Chain D: Q.172 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:Q.172, A:N.45 NAG.4: 3 residues within 4Å: Chain A: N.392, G.408, K.409 No protein-ligand interaction detected (PLIP) NAG.5: 2 residues within 4Å: Chain C: T.16, N.79 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.16, C:T.16 NAG.7: 2 residues within 4Å: Chain D: E.73, N.77 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.73, D:N.77 NAG.8: 4 residues within 4Å: Chain D: N.45, N.133, N.158 Chain G: Q.172 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain D Hydrogen bonds: G:Q.172, D:N.45 NAG.9: 3 residues within 4Å: Chain D: N.392, G.408, K.409 No protein-ligand interaction detected (PLIP) NAG.10: 2 residues within 4Å: Chain F: T.16, N.79 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:T.16, F:T.16 NAG.12: 2 residues within 4Å: Chain G: E.73, N.77 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:E.73, G:N.77 NAG.13: 4 residues within 4Å: Chain A: Q.172 Chain G: N.45, N.133, N.158 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain G Hydrogen bonds: A:Q.172, G:N.45 NAG.14: 3 residues within 4Å: Chain G: N.392, G.408, K.409 No protein-ligand interaction detected (PLIP) NAG.15: 2 residues within 4Å: Chain I: T.16, N.79 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:T.16, I:T.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Avanzato, V.A. et al., A structural basis for antibody-mediated neutralization of Nipah virus reveals a site of vulnerability at the fusion glycoprotein apex. Proc.Natl.Acad.Sci.USA (2019)

Release Date

2019-11-27

Peptides

Fusion glycoprotein F0: ADG
Fab66 light chain: BEH
Fab66 heavy chain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

D
F

G
F

B
L

E
L

H
L

C
H

F
H

I
H

Fusion glycoprotein F0

Fab66 light chain

Fab66 heavy chain