MolNFT v1 · #148412 · protein
Crystal structure of ebolavirus glycoprotein in complex with bepridil
6F5U · Envelope GLYCOPROTEIN,ENVELOPE GLYCOPROTEIN,GP1: “Crystal structure of ebolavirus glycoprotein in complex with bepridil”. X-ray diffraction, 4 ligands (CQN, NAG, BMA), 5 pockets (best druggability 0.64). MolNFT v1 #148412 on…
- PDB
- 6F5U
- Type
- protein
- Length
- 381 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
- Ligands
- CQN, NAG, BMA, MAN
- Pockets
- 5 · best druggability 0.64
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 | 10% helix, 38% strand | Q05320 |
| B | Envelope glycoprotein | protein | 131 | 42% helix, 10% strand | Q05320 |
Ligands and binding sites
- CQN · Bepridil · 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 · 5 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.64 | 0.80 | 36 | GOL, DMS |
| 2 | 225 | 0.56 | 0.78 | 31 | CQN |
| 3 | 122 | 0.47 | 0.79 | 28 | empty |
| 4 | 115 | 0.40 | 0.76 | 18 | empty |
| 5 | 98 | 0.40 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2658 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6F5U · Crystal structure of ebolavirus glycoprotein in complex with bepridil · 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 6F5U · PDBe 6F5U · UniProt Q05320
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