SMTL ID : 5evm.1 (1 other biounit)

Crystal Structure of Nipah Virus Fusion Glycoprotein in the Prefusion State

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.37 Å

Oligo State

homo-trimer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-[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: 4 residues within 4Å: Chain A: N.414, G.430, K.431 Chain B: V.118 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-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-NAG.8: 4 residues within 4Å: Chain A: Q.459, M.463 Chain C: N.464, Q.468 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain C: E.95, N.99 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-MAN.3: 4 residues within 4Å: Chain A: N.464, Q.468 Chain B: Q.459, M.463 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.4: 3 residues within 4Å: Chain B: N.414, G.430 Chain C: V.118 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.5: 2 residues within 4Å: Chain B: E.95, N.99 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-MAN-MAN-MAN.6: 5 residues within 4Å: Chain B: N.464, Q.468 Chain C: D.304, P.448, Q.459 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-MAN-MAN-MAN.7: 5 residues within 4Å: Chain A: V.118 Chain C: N.414, L.429, G.430, K.431 No protein-ligand interaction detected (PLIP)

3 x MLI: MALONATE ION(Non-functional Binders)

MLI.10: 7 residues within 4Å: Chain A: T.173, A.174, L.175, D.177, F.235, N.238 Chain B: L.201 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.235 Hydrogen bonds: A:L.175, A:N.238 MLI.11: 5 residues within 4Å: Chain B: A.174, L.175, F.235, N.238 Chain C: L.201 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.235 Hydrogen bonds: B:L.175, B:N.238 MLI.12: 5 residues within 4Å: Chain A: L.201 Chain C: A.174, L.175, F.235, N.238 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.235 Hydrogen bonds: C:T.173, C:L.175, C:N.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, K. et al., Crystal Structure of the Pre-fusion Nipah Virus Fusion Glycoprotein Reveals a Novel Hexamer-of-Trimers Assembly. Plos Pathog. (2015)

Release Date

2015-12-16

Peptides

Fusion glycoprotein F0: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Fusion glycoprotein F0

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