Research workbench
Crystal structure of ebolavirus glycoprotein in complex with clomipramine
Analyse Crystal structure of ebolavirus glycoprotein in complex with clomipramine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6G9I
- Type
- protein
- Length
- 381 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope GLYCOPROTEIN,ENVELOPE glycoprotein
- UniProt
- Q05320, M1E1E4
- Ligands
- CXX, NAG, BMA, MAN
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope GLYCOPROTEIN,ENVELOPE glycoprotein | protein | 251 | 12% helix, 40% strand | Q05320 |
| B | Envelope GLYCOPROTEIN,ENVELOPE glycoprotein | protein | 130 | 38% helix, 12% strand | Q05320, M1E1E4 |
Ligands and binding sites
- CXX · 3-(3-chloro-5H-dibenzo[b,f]azepin-5-yl)-N,N-dimethylpropan-1-amine · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.56 | 0.79 | 30 | CXX |
| 2 | 207 | 0.55 | 0.79 | 30 | empty |
| 3 | 129 | 0.42 | 0.76 | 20 | empty |
| 4 | 97 | 0.40 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2709 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6G9I · Crystal structure of Ebolavirus glycoprotein in complex with clomipramine · 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 M1E1E4
- Elsewhere: RCSB PDB 6G9I · PDBe 6G9I · UniProt Q05320 · UniProt M1E1E4
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