Research workbench
Crystal structure of ebolavirus glycoprotein in complex with benztropine
Analyse Crystal structure of ebolavirus glycoprotein in complex with benztropine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F6S
- Type
- protein
- Length
- 379 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
- CXQ, NAG
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope GLYCOPROTEIN,ENVELOPE GLYCOPROTEIN,GP1 | protein | 250 | 11% helix, 40% strand | Q05320 |
| B | Envelope glycoprotein | protein | 129 | 41% helix, 9% strand | A0A0U3BWW0 |
Ligands and binding sites
- CXQ · benztropine · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 13 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.57 | 0.80 | 24 | CXQ |
| 2 | 120 | 0.45 | 0.78 | 22 | DMS |
| 3 | 103 | 0.41 | 0.77 | 16 | empty |
| 4 | 54 | 0.40 | 0.81 | 19 | empty |
| 5 | 113 | 0.40 | 0.75 | 17 | DMS |
Interfaces
1 interface between chains.
- A–B · 2597 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6F6S · CRYSTAL STRUCTURE OF EBOLAVIRUS GLYCOPROTEIN IN COMPLEX WITH benztropine · 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 6F6S · PDBe 6F6S · UniProt Q05320 · UniProt A0A0U3BWW0
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