MolNFT v1 · #123621 · protein
Crystal structure of ebola glycoprotein
5JQ3 · Envelope glycoprotein 1,ENVELOPE glycoprotein 1,ENVELOPE…: “Crystal structure of ebola glycoprotein”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 8 pockets (best druggability 0.60). MolNFT v1 #123621 on GenesisL1: 3D structure…
- PDB
- 5JQ3
- Type
- protein
- Length
- 393 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein 1,ENVELOPE glycoprotein 1,ENVELOPE glycoprotein 1; Envelope…
- UniProt
- Q05320
- Ligands
- NAG, MAN, BMA
- Pockets
- 8 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein 1,ENVELOPE glycoprotein 1,ENVELOPE glycoprotein 1 | protein | 263 | 10% helix, 39% strand | Q05320 |
| B | Envelope glycoprotein 2 | protein | 130 | 41% helix, 12% strand | Q05320 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.60 | 0.83 | 27 | empty |
| 2 | 217 | 0.59 | 0.80 | 30 | empty |
| 3 | 103 | 0.39 | 0.76 | 16 | empty |
| 4 | 62 | 0.39 | 0.80 | 13 | empty |
| 5 | 108 | 0.39 | 0.75 | 19 | GOL |
Interfaces
1 interface between chains.
- A–B · 2866 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 5JQ3 · Crystal structure of Ebola 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 Q05320
- Elsewhere: RCSB PDB 5JQ3 · PDBe 5JQ3 · UniProt Q05320
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