Research workbench
Crystal structure of ebolavirus glycoprotein in complex with sertraline
Analyse Crystal structure of ebolavirus glycoprotein in complex with sertraline in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F6N
- Type
- protein
- Length
- 384 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope GLYCOPROTEIN,ENVELOPE GLYCOPROTEIN,GP1; Envelope glycoprotein
- UniProt
- Q05320, A0A0U3BWW0
- Ligands
- SRE, NAG, MAN, BMA
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope GLYCOPROTEIN,ENVELOPE GLYCOPROTEIN,GP1 | protein | 253 | 11% helix, 39% strand | Q05320 |
| B | Envelope glycoprotein | protein | 131 | 37% helix, 10% strand | A0A0U3BWW0 |
Ligands and binding sites
- SRE · (1S,4S)-4-(3,4-dichlorophenyl)-N-methyl-1,2,3,4-tetrahydronaphthalen-1-amine · 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
- DMS · Dimethyl sulfoxide · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 262 | 0.58 | 0.78 | 30 | SRE |
| 2 | 177 | 0.53 | 0.78 | 29 | empty |
| 3 | 51 | 0.39 | 0.81 | 13 | empty |
| 4 | 99 | 0.38 | 0.75 | 15 | empty |
| 5 | 87 | 0.37 | 0.76 | 17 | DMS |
Interfaces
1 interface between chains.
- A–B · 2681 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6F6N · Crystal structure of ebolavirus glycoprotein in complex with sertraline · 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
- Every structure of UniProt A0A0U3BWW0
- Elsewhere: RCSB PDB 6F6N · PDBe 6F6N · UniProt Q05320 · UniProt A0A0U3BWW0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.