SMTL ID : 6c5v.1

An anti-gH/gL antibody that neutralizes dual-tropic infection defines a site of vulnerability on Epstein-Barr virus

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.1: 3 residues within 4Å: Chain A: N.67, R.215 Chain E: S.66 No protein-ligand interaction detected (PLIP)

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

NAG.2: 2 residues within 4Å: Chain A: N.442, V.443 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.443 NAG.3: 3 residues within 4Å: Chain A: I.555, N.556, M.591 No protein-ligand interaction detected (PLIP) NAG.4: 2 residues within 4Å: Chain A: N.671 Chain C: K.40 No protein-ligand interaction detected (PLIP) NAG.5: 2 residues within 4Å: Chain B: E.45, N.46 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.45 Hydrogen bonds: B:E.45, B:E.45, B:E.45 NAG.6: 3 residues within 4Å: Chain A: E.37 Chain B: N.55, S.119 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.37 NAG.7: 2 residues within 4Å: Chain C: N.55, N.57 No protein-ligand interaction detected (PLIP) NAG.8: 1 residues within 4Å: Chain C: N.91 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.91 NAG.9: 2 residues within 4Å: Chain C: N.166, T.174 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Snijder, J. et al., An Antibody Targeting the Fusion Machinery Neutralizes Dual-Tropic Infection and Defines a Site of Vulnerability on Epstein-Barr Virus. Immunity (2018)

Release Date

2018-05-02

Peptides

Envelope glycoprotein H: A
Envelope glycoprotein L: B
Glycoprotein 42: C
Antibody Fab AMMO1 heavy chain: D
Antibody Fab AMMO1 light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
L

Envelope glycoprotein H

Envelope glycoprotein L

Glycoprotein 42

Antibody Fab AMMO1 heavy chain

Antibody Fab AMMO1 light chain

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