SMTL ID : 8xps.1

Structure of Nipah virus Bangladesh string G protein ectodomain monomer bound to single-domain antibody n425 at 3.22 Angstroms overall resolution

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 5 residues within 4Å: Chain B: T.361, K.415, N.417, S.419, D.420 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-MAN-MAN-MAN.2: 3 residues within 4Å: Chain B: V.300, N.306, Y.309 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.309

2 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.3: 3 residues within 4Å: Chain B: N.195, I.197, T.602 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.4: 1 residues within 4Å: Chain B: N.529 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-MAN-MAN.5: 2 residues within 4Å: Chain B: N.378, S.380 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y. et al., Fully human single-domain antibody targeting a highly conserved cryptic epitope on the Nipah virus G protein. Nat Commun (2024)

Release Date

2024-09-18

Peptides

single-domain antibody n425: A
Nipah virus Bangladesh string G protein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

single-domain antibody n425

Nipah virus Bangladesh string G protein

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