Research workbench
Crystal structure of sudan ebolavirus glycoprotein (strain boniface) bound to 16F6
Analyse Crystal structure of sudan ebolavirus glycoprotein (strain boniface) bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VE0
- Type
- protein
- Length
- 782 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein; 16F6 antibody chain a; 16F6 antibody chain B
- UniProt
- Q66814
- Ligands
- NAG, MAN
- Pockets
- 14 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | Envelope glycoprotein | protein | 245 | 7% helix, 33% strand | Q66814 |
| J | Envelope glycoprotein | protein | 105 | 33% helix, 13% strand | Q66814 |
| A | 16F6 antibody chain a | protein | 220 | 4% helix, 50% strand | — |
| B | 16F6 antibody chain B | protein | 212 | 5% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains I, J
- MAN · alpha-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.71 | 0.86 | 32 | empty |
| 2 | 636 | 0.70 | 0.78 | 70 | empty |
| 3 | 74 | 0.57 | 0.88 | 23 | empty |
| 4 | 174 | 0.57 | 0.81 | 30 | empty |
| 5 | 313 | 0.56 | 0.75 | 32 | empty |
Interfaces
6 interfaces between chains.
- I–J · 2440 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1736 Ų buried · 16 hydrogen bonds · protein-protein
- I–A · 376 Ų buried · 5 hydrogen bonds · protein-protein
- J–A · 247 Ų buried · 3 hydrogen bonds · protein-protein
- J–B · 159 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 9 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3VE0 · Crystal structure of Sudan Ebolavirus Glycoprotein (strain Boniface) bound to 16F6 · the same entry in another collection · chain I against I, 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 Q66814
- Elsewhere: RCSB PDB 3VE0 · PDBe 3VE0 · UniProt Q66814
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.