Research workbench
Gp41-targeting HIV-1 fusion inhibitors with hook-like Ile-Asp-Leu tail
Analyse Gp41-targeting HIV-1 fusion inhibitors with hook-like Ile-Asp-Leu tail in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HFM
- Type
- protein
- Length
- 458 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.298
- Source
- Human immunodeficiency virus 1
- Molecule
- Envelope glycoprotein gp160,gp41 CHR region
- UniProt
- Q70626
- Ligands
- TAM
- Pockets
- 1 · best druggability 0.52
Structure
x-ray diffraction · resolution 2.298 · 2 distinct chains · 84% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E | Envelope glycoprotein gp160,gp41 CHR region | protein | 77 | 82% helix, 0% strand | Q70626 |
| B, F | Envelope glycoprotein gp160,gp41 CHR region | protein | 75 | 85% helix, 0% strand | Q70626 |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · 2 copies · chains B, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 244 | 0.52 | 0.76 | 21 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1319 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 1304 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 1301 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 1300 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 1291 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5HFM · GP41-targeting HIV-1 fusion inhibitors with hook-like ile-asp-leu tail · 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 Q70626
- Elsewhere: RCSB PDB 5HFM · PDBe 5HFM · UniProt Q70626
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