SMTL ID : 7upd.1

Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2B12

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

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

NAG.1: 5 residues within 4Å: Chain A: N.67, N.155, E.156, N.180 Chain D: Q.194 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:N.155, D:Q.194 NAG.2: 2 residues within 4Å: Chain A: E.95, N.99 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.95 NAG.3: 3 residues within 4Å: Chain A: N.414, G.430, K.431 No protein-ligand interaction detected (PLIP) NAG.4: 4 residues within 4Å: Chain A: N.464, Q.468 Chain D: Q.459, M.463 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:Q.468, D:Q.459 Hydrophobic interactions: D:Q.459 NAG.5: 5 residues within 4Å: Chain D: N.67, N.155, E.156, N.180 Chain G: Q.194 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain G Hydrogen bonds: D:N.155, G:Q.194 NAG.6: 2 residues within 4Å: Chain D: E.95, N.99 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.95 NAG.7: 4 residues within 4Å: Chain D: N.414, G.430, K.431 Chain G: V.118 No protein-ligand interaction detected (PLIP) NAG.8: 4 residues within 4Å: Chain D: N.464, Q.468 Chain G: Q.459, M.463 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain D Hydrophobic interactions: G:Q.459 Hydrogen bonds: G:Q.459, D:Q.468 NAG.9: 5 residues within 4Å: Chain A: Q.194 Chain G: N.67, N.155, E.156, N.180 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain A Hydrogen bonds: G:N.155, A:Q.194 NAG.10: 2 residues within 4Å: Chain G: E.95, N.99 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:E.95 NAG.11: 3 residues within 4Å: Chain G: N.414, G.430, K.431 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:K.431 NAG.12: 4 residues within 4Å: Chain A: Q.459, M.463 Chain G: N.464, Q.468 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.459 Hydrogen bonds: A:Q.459

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Byrne, P.O. et al., Structural basis for antibody recognition of vulnerable epitopes on Nipah virus F protein. Nat Commun (2023)

Release Date

2023-03-29

Peptides

Fusion glycoprotein F0: ADG
Fab 2B12 heavy chain: BCH
Fab 2B12 light chain: EFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

G
G

B
B

C
C

H
H

E
E

F
F

I
L

Fusion glycoprotein F0

Fab 2B12 heavy chain

Fab 2B12 light chain