MolNFT v1 · #151584 · protein
Crystal structure of ebolavirus glycoprotein in complex with inhibitor 118
6HS4 · Envelope GLYCOPROTEIN,GP1,ENVELOPE glycoprotein: “Crystal structure of ebolavirus glycoprotein in complex with inhibitor 118”. X-ray diffraction, 4 ligands (GON, NAG, MAN), 6 pockets (best druggability 0.57). MolNFT v1 #151584 on…
- PDB
- 6HS4
- Type
- protein
- Length
- 388 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope GLYCOPROTEIN,GP1,ENVELOPE glycoprotein; Envelope glycoprotein
- UniProt
- Q05320
- Ligands
- GON, NAG, MAN, BMA
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope GLYCOPROTEIN,GP1,ENVELOPE glycoprotein | protein | 258 | 11% helix, 40% strand | Q05320 |
| B | Envelope glycoprotein | protein | 130 | 41% helix, 12% strand | Q05320 |
Ligands and binding sites
- GON · 1-[2-[3-oxidanyl-4-(4-phenyl-1~{H}-pyrazol-5-yl) phenoxy]ethyl]piperidine-4-carboxamide · ligand · 2 copies · chains A, B
- 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 · 3 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.57 | 0.78 | 33 | GON |
| 2 | 206 | 0.54 | 0.78 | 24 | empty |
| 3 | 107 | 0.40 | 0.76 | 20 | GOL |
| 4 | 98 | 0.40 | 0.76 | 16 | empty |
| 5 | 56 | 0.37 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2789 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 6HS4 · Crystal structure of Ebolavirus glycoprotein in complex with inhibitor 118 · 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 6HS4 · PDBe 6HS4 · UniProt Q05320
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