SMTL ID : 8sgn.1

Crystal structure of Epstein-Barr virus glycoprotein 350 (gp350) in complex with Cy651H02, a monoclonal antibody isolated from macaques immunized with a gp350 nanoparticle vaccine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 8 residues within 4Å: Chain C: D.45, N.47, D.62, L.63, D.64, G.80, A.81, F.82 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:D.62 Hydrogen bonds: C:G.80, C:F.82, C:D.45

23 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 3 residues within 4Å: Chain A: R.106, K.170, Y.176 Ligand excluded by PLIP EDO.3: 1 residues within 4Å: Chain A: R.56 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: V.159, N.160, A.161 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain A: N.173, K.175 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: G.30, K.68, G.70 Chain C: P.149, V.150 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: T.166, K.167 Chain B: V.176, L.177 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: R.56, P.57, V.60 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain B: S.25, G.26 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain B: S.66, R.67 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain B: K.13, S.122, T.123 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain B: R.100 Chain C: E.214, D.215 Ligands: TRS.15 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain B: P.112, G.113 Ligands: EDO.19 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain B: S.7, G.8, P.9, G.10, V.114, L.115, K.208 Ligand excluded by PLIP EDO.19: 2 residues within 4Å: Chain B: E.155 Ligands: EDO.17 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain B: S.30, Y.32, G.52, N.53, G.54, G.55 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain C: E.217, I.218, S.219 Ligand excluded by PLIP EDO.31: 2 residues within 4Å: Chain C: N.87, T.89 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain C: S.124, L.125, M.146, P.149, V.150, L.152, Y.235 Ligand excluded by PLIP EDO.33: 2 residues within 4Å: Chain C: P.310, S.312 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain C: N.87, N.90, R.107, K.110 Ligand excluded by PLIP EDO.35: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.36: 2 residues within 4Å: Chain C: G.326, K.423 Ligand excluded by PLIP EDO.37: 5 residues within 4Å: Chain C: P.316, T.317, N.318, T.415 Ligands: NAG.22 Ligand excluded by PLIP

4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 2 residues within 4Å: Chain A: Q.16, S.17 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.16, A:S.17, A:S.17 TRS.5: 2 residues within 4Å: Chain A: Q.188, H.192 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.188 TRS.6: 3 residues within 4Å: Chain A: S.61, R.63, Q.81 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.61, A:S.61, A:R.63, A:Q.81, A:E.83 TRS.15: 6 residues within 4Å: Chain B: Q.1, L.2, G.26, R.98, R.100 Ligands: EDO.16 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.2, B:G.26, B:R.98, B:R.100

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

NAG.21: 5 residues within 4Å: Chain C: N.277, V.304, F.305, S.306, D.307 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:V.304 Hydrogen bonds: C:N.277, C:F.305, C:F.305, C:D.307, C:D.307 NAG.22: 7 residues within 4Å: Chain C: N.318, T.320, Y.331, S.332, P.334, H.417 Ligands: EDO.37 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.318, C:T.320, C:S.332, C:H.417 NAG.23: 2 residues within 4Å: Chain C: K.227, N.229 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:K.227 Hydrogen bonds: C:N.229, C:N.229 Water bridges: C:N.229 NAG.24: 3 residues within 4Å: Chain C: N.356, N.357, T.360 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:N.357 NAG.25: 5 residues within 4Å: Chain C: G.83, G.84, S.85, E.86, N.114 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:E.86 Hydrogen bonds: C:G.83, C:E.86, C:E.86 NAG.26: 5 residues within 4Å: Chain C: C.8, Q.9, P.344, N.345, T.410 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:P.344 Hydrogen bonds: C:Q.9, C:N.345 NAG.27: 5 residues within 4Å: Chain C: A.384, S.385, N.386, T.388, D.390 No protein-ligand interaction detected (PLIP) NAG.28: 2 residues within 4Å: Chain C: E.86, N.87 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:E.86 NAG.29: 8 residues within 4Å: Chain B: R.56 Chain C: N.164, C.165, N.166, D.296, Y.297, C.298, I.299 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.166, C:D.296, C:C.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joyce, M.G. et al., Crystal structure of Epstein-Barr virus glycoprotein 350 (gp350) in complex with Cy651H02, a monoclonal antibody isolated from macaques immunized with a gp350 nanoparticle vaccine. To Be Published

Release Date

2024-04-17

Peptides

Cy651H02 Fab light chain: A
Cy651H02 Fab heavy chain: B
Envelope glycoprotein gp350: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
G

Cy651H02 Fab light chain

Cy651H02 Fab heavy chain

Envelope glycoprotein gp350

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