Research workbench
Crystal structure of ebola glycoprotein in complex with ibuprofen
Analyse Crystal structure of ebola glycoprotein in complex with ibuprofen in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JQB
- Type
- protein
- Length
- 388 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
- IBP, NAG, BMA
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein 1,ENVELOPE glycoprotein 1,ENVELOPE glycoprotein 1 | protein | 257 | 10% helix, 38% strand | Q05320 |
| B | Envelope glycoprotein 2 | protein | 131 | 42% helix, 11% strand | Q05320 |
Ligands and binding sites
- IBP · Ibuprofen · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 252 | 0.62 | 0.80 | 32 | IBP |
| 2 | 227 | 0.58 | 0.79 | 32 | empty |
| 3 | 127 | 0.40 | 0.75 | 19 | GOL |
| 4 | 103 | 0.39 | 0.76 | 15 | empty |
| 5 | 50 | 0.33 | 0.78 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 2805 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 5JQB · Crystal structure of Ebola glycoprotein in complex with ibuprofen · 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 5JQB · PDBe 5JQB · UniProt Q05320
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