Research workbench
Epstein barr virus major envelope glycoprotein
Analyse Epstein barr virus major envelope glycoprotein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H6O
- Type
- protein
- Length
- 440 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major outer envelope glycoprotein GP350
- UniProt
- Q9QP87
- Ligands
- MAN, NAG, BMA, GAL, NDG, FUC
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major outer envelope glycoprotein GP350 | protein | 440 | 3% helix, 38% strand | Q9QP87 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 57 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 27 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A
- GAL · beta-D-galactopyranose · sugar · 6 copies
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 3 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.49 | 0.87 | 18 | empty |
| 2 | 118 | 0.42 | 0.77 | 27 | empty |
| 3 | 65 | 0.36 | 0.78 | 15 | empty |
| 4 | 63 | 0.32 | 0.76 | 18 | empty |
Modifications
Observed in the structure: 10 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 2H6O · Epstein Barr Virus Major Envelope Glycoprotein · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9QP87
- Elsewhere: RCSB PDB 2H6O · PDBe 2H6O · UniProt Q9QP87
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