Research workbench
Crystal structure of ebolavirus glycoprotein in complex with imipramine
Analyse Crystal structure of ebolavirus glycoprotein in complex with imipramine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6G9B
- Type
- protein
- Length
- 381 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope GLYCOPROTEIN,ENVELOPE glycoprotein; Envelope glycoprotein
- UniProt
- Q05320
- Ligands
- IXX, NAG
- Pockets
- 6 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope GLYCOPROTEIN,ENVELOPE glycoprotein | protein | 253 | 11% helix, 40% strand | Q05320 |
| B | Envelope glycoprotein | protein | 128 | 42% helix, 12% strand | Q05320 |
Ligands and binding sites
- IXX · 3-(5H-dibenzo[b,f]azepin-5-yl)-N,N-dimethylpropan-1-amine · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 3 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 | 207 | 0.56 | 0.79 | 23 | IXX |
| 2 | 159 | 0.47 | 0.77 | 22 | empty |
| 3 | 64 | 0.41 | 0.80 | 13 | empty |
| 4 | 105 | 0.41 | 0.76 | 16 | empty |
| 5 | 98 | 0.39 | 0.76 | 18 | GOL |
Interfaces
1 interface between chains.
- A–B · 2769 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6G9B · Crystal structure of Ebolavirus glycoprotein in complex with imipramine · 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 6G9B · PDBe 6G9B · UniProt Q05320
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