SMTL ID : 7up9.1

Prefusion-stabilized Nipah virus fusion protein complexed with Fab 2D3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-mer

Ligands

1 x NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG.1: 7 residues within 4Å: Chain A: D.188, K.189, I.190, P.191, C.192 Chain C: N.67, V.184 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.188, A:D.188, A:C.192

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

NAG.2: 3 residues within 4Å: Chain A: N.67, N.155, V.184 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.184 Hydrogen bonds: A:N.155 NAG.3: 2 residues within 4Å: Chain A: E.95, N.99 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.95, A:E.95, A:N.99 NAG.4: 3 residues within 4Å: Chain A: N.414, G.430, K.431 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.431 NAG.5: 3 residues within 4Å: Chain A: N.464, Q.468 Chain B: Q.459 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.459 NAG.6: 1 residues within 4Å: Chain B: N.67 No protein-ligand interaction detected (PLIP) NAG.7: 1 residues within 4Å: Chain B: N.99 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.99 NAG.8: 3 residues within 4Å: Chain B: N.414, G.430, K.431 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.431 NAG.9: 4 residues within 4Å: Chain B: N.464, Q.468 Chain C: Q.459, M.463 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Q.468, C:Q.459 Hydrophobic interactions: C:Q.459 NAG.10: 2 residues within 4Å: Chain C: I.96, N.99 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.96 Hydrogen bonds: C:N.99 NAG.11: 3 residues within 4Å: Chain C: N.414, G.430, K.431 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.431 NAG.12: 3 residues within 4Å: Chain A: Q.459 Chain C: N.464, Q.468 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Q.468 Hydrophobic interactions: 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: ABC
Fab 2D3 heavy chain: D
Fab 2D3 light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
G

D
H

E
L

Fusion glycoprotein F0

Fab 2D3 heavy chain

Fab 2D3 light chain

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