SMTL ID : 7ki4.1

Structure of the NiV F glycoprotein in complex with the 12B2 neutralizing antibody

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

6 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: 2 residues within 4Å: Chain A: E.95, N.99 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.414, G.430, K.431 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain D: E.95, N.99 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain D: N.414, G.430, K.431 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain G: E.95, N.99 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain G: N.414, G.430, K.431 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA.2: 4 residues within 4Å: Chain A: N.464, Q.468 Chain D: P.448, Q.459 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 4 residues within 4Å: Chain D: N.464, Q.468 Chain G: P.448, Q.459 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 4 residues within 4Å: Chain A: P.448, Q.459 Chain G: N.464, Q.468 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-FUC.4: 12 residues within 4Å: Chain A: S.66, N.67, S.69 Chain B: E.56 Chain C: Q.1, V.2, G.26, Y.32, R.97, R.99, G.100, Y.108 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:E.56, C:Q.1 NAG-NAG-BMA-MAN-MAN-FUC.8: 12 residues within 4Å: Chain D: S.66, N.67, S.69 Chain E: E.56 Chain F: Q.1, V.2, G.26, Y.32, R.97, R.99, G.100, Y.108 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:E.56, F:Q.1 NAG-NAG-BMA-MAN-MAN-FUC.12: 12 residues within 4Å: Chain G: S.66, N.67, S.69 Chain H: E.56 Chain I: Q.1, V.2, G.26, Y.32, R.97, R.99, G.100, Y.108 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain I Hydrogen bonds: H:E.56, I:Q.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dang, H.V. et al., Broadly neutralizing antibody cocktails targeting Nipah virus and Hendra virus fusion glycoproteins. Nat.Struct.Mol.Biol. (2021)

Release Date

2021-05-05

Peptides

Fusion glycoprotein F0: ADG
12B2 Fab light chain: BEH
12B2 heavy chain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
E

B
L

E
C

H
F

C
H

F
D

I
G

Fusion glycoprotein F0

12B2 Fab light chain

12B2 heavy chain