MolNFT v1 · #151569 · protein
Crystal structure of ebolavirus glycoprotein in complex with inhibitor 118A
6HRO · Envelope GLYCOPROTEIN,ENVELOPE GLYCOPROTEIN,ENVELOPE…: “Crystal structure of ebolavirus glycoprotein in complex with inhibitor 118A”. X-ray diffraction, 4 ligands (GKZ, NAG, MAN), 7 pockets (best druggability 0.67). MolNFT v1…
- PDB
- 6HRO
- Type
- protein
- Length
- 388 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope GLYCOPROTEIN,ENVELOPE GLYCOPROTEIN,ENVELOPE glycoprotein; Envelope glycoprotein
- UniProt
- Q05320
- Ligands
- GKZ, NAG, MAN, BMA
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope GLYCOPROTEIN,ENVELOPE GLYCOPROTEIN,ENVELOPE glycoprotein | protein | 258 | 11% helix, 40% strand | Q05320 |
| B | Envelope glycoprotein | protein | 130 | 41% helix, 12% strand | Q05320 |
Ligands and binding sites
- GKZ · 1-[2-[4-[4-(4-chlorophenyl)-3-methyl-1~{H}-pyrazol-5-yl]-3-oxidanyl-phenoxy]ethyl]piperidin-1-ium-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 · 4 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
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 361 | 0.67 | 0.80 | 32 | GKZ |
| 2 | 141 | 0.50 | 0.79 | 28 | empty |
| 3 | 75 | 0.43 | 0.80 | 17 | empty |
| 4 | 95 | 0.41 | 0.77 | 20 | empty |
| 5 | 97 | 0.39 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2854 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 6HRO · Crystal structure of Ebolavirus glycoprotein in complex with inhibitor 118a · 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 6HRO · PDBe 6HRO · UniProt Q05320
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