SMTL ID : 8sic.1 (1 other biounit)

Crystal structure of Epstein-Barr virus glycoprotein 350 (gp350) in complex with Cy137C02, a monoclonal antibody isolated from macaques immunized with a gp350 nanoparticle vaccine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.76 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain C: D.45, V.46, N.47 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:N.47 Water bridges: C:N.47, C:N.47 NAG.2: 6 residues within 4Å: Chain C: L.6, C.8, Q.9, P.344, N.345, T.410 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.6 NAG.3: 4 residues within 4Å: Chain C: A.384, S.385, N.386, T.388 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.385, C:T.388 NAG.4: 4 residues within 4Å: Chain C: F.82, G.83, N.114, V.115 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.115 Hydrogen bonds: C:Q.60, C:N.114 NAG.5: 1 residues within 4Å: Chain C: N.318 No protein-ligand interaction detected (PLIP) NAG.6: 2 residues within 4Å: Chain C: D.215, N.229 No protein-ligand interaction detected (PLIP) NAG.8: 4 residues within 4Å: Chain C: Q.13, D.340, T.410, N.411 No protein-ligand interaction detected (PLIP) NAG.9: 7 residues within 4Å: Chain A: V.56 Chain C: N.164, N.166, S.186, D.296, Y.297, C.298 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.186, C:C.298

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 2 residues within 4Å: Chain C: H.426, H.429 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.426, C:H.429

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joyce, M.G. et al., Structural basis for complement receptor engagement and virus neutralization through Epstein-Barr virus gp350. Immunity (2025)

Release Date

2024-04-17

Peptides

Cy137C02 Fab heavy chain: A
Cy137C02 Fab light chain: B
Envelope glycoprotein gp350: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

Cy137C02 Fab heavy chain

Cy137C02 Fab light chain

Envelope glycoprotein gp350

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