SMTL ID : 9b9e.1

Prefusion F glycoprotein ectodomain of Nipah virus ectodomain in complex with DS90 nanobody

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: N.438, Q.442 Chain B: Q.433, M.437 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.442, B:Q.433 Hydrophobic interactions: B:M.437 NAG.2: 2 residues within 4Å: Chain A: N.73, N.74 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.73 NAG.3: 3 residues within 4Å: Chain A: N.388, G.404, K.405 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.405 NAG.4: 2 residues within 4Å: Chain A: N.41, V.158 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.158 Hydrogen bonds: A:N.41 NAG.5: 3 residues within 4Å: Chain B: N.388, G.404, K.405 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.405 NAG.6: 1 residues within 4Å: Chain B: N.73 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.73 NAG.7: 4 residues within 4Å: Chain B: N.438, Q.442 Chain C: Q.433, M.437 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Q.442, C:Q.433 Hydrophobic interactions: C:M.437 NAG.8: 2 residues within 4Å: Chain B: N.41, V.158 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.158 Hydrogen bonds: B:N.41 NAG.9: 3 residues within 4Å: Chain C: N.388, G.404, K.405 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.405 NAG.10: 2 residues within 4Å: Chain C: E.69, N.73 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.73 NAG.11: 4 residues within 4Å: Chain A: Q.433, M.437 Chain C: N.438, Q.442 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:M.437 Hydrogen bonds: A:Q.433, C:Q.442 NAG.12: 2 residues within 4Å: Chain A: Q.168 Chain C: N.41 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Low, Y.S. et al., Prefusion F glycoprotein ectodomain of Nipah virus ectodomain in complex with DS90 nanobody. To Be Published

Release Date

2025-06-04

Peptides

Fusion glycoprotein F0: ABC
DS90 nanobody: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Fusion glycoprotein F0

DS90 nanobody