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Crystal Structure of Ebola zaire GP protein with bound ARN0074898
Analyse Crystal Structure of Ebola zaire GP protein with bound ARN0074898 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NAE
- Type
- protein
- Length
- 355 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.75
- Source
- Zaire ebolavirus (strain Mayinga-76)
- Molecule
- Envelope glycoprotein,Envelope glycoprotein,Envelope glycoprotein; Envelope glycoprotein
- UniProt
- Q05320
- Ligands
- KHG, NAG, MAN, BMA
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · resolution 2.75 · 2 distinct chains · 20% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein,Envelope glycoprotein,Envelope glycoprotein | protein | 238 | 11% helix, 39% strand | Q05320 |
| B | Envelope glycoprotein | protein | 117 | 39% helix, 10% strand | Q05320 |
Ligands and binding sites
- KHG · (1S,3R,5R,7S)-N-(trans-4-aminocyclohexyl)-3-methyl-5-phenyltricyclo[3.3.1.1~3,7~]decane-1-carboxamide · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- 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 | 140 | 0.59 | 0.83 | 25 | GOL |
| 2 | 200 | 0.56 | 0.79 | 26 | KHG |
| 3 | 109 | 0.40 | 0.76 | 17 | empty |
| 4 | 86 | 0.38 | 0.76 | 17 | empty |
| 5 | 78 | 0.35 | 0.76 | 20 | GOL |
Interfaces
1 interface between chains.
- A–B · 2687 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6NAE · Crystal structure of ebola zaire gp protein with bound ARN0074898 · 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 6NAE · PDBe 6NAE · UniProt Q05320
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