Research workbench
Asymmetric structure of cleaved HIV-1 AD8 envelope glycoprotein trimer in styrene-maleic acid lipid nanoparticles
Analyse Asymmetric structure of cleaved HIV-1 AD8 envelope glycoprotein trimer in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8FAD
- Type
- protein
- Length
- 1,797 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.0
- Source
- Human immunodeficiency virus 1
- Molecule
- Transmembrane protein gp41; Envelope glycoprotein gp120
- UniProt
- P19550, B0FDK7
- Ligands
- 83G, NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · resolution 4.0 · 3 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | Transmembrane protein gp41 | protein | 138 | 66% helix, 2% strand | P19550 |
| C, E, A | Envelope glycoprotein gp120 | protein | 466 | 14% helix, 33% strand | B0FDK7 |
| F | Transmembrane protein gp41 | protein | 123 | 59% helix, 5% strand | P19550 |
Ligands and binding sites
- 83G · 1-[(2R)-4-(benzenecarbonyl)-2-methylpiperazin-1-yl]-2-(4-methoxy-1H-pyrrolo[2,3-b]pyridin-3-yl)ethane-1,2-dione · ligand · 3 copies · chains C, E, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 118 copies · chains B, C, D, E, F, A
- BMA · beta-D-mannopyranose · sugar · 13 copies · chains C, E
- MAN · alpha-D-mannopyranose · sugar · 11 copies · chains C, E, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.89 | 0.94 | 108 | empty |
| 2 | 515 | 0.87 | 0.93 | 78 | empty |
| 3 | 495 | 0.82 | 0.88 | 48 | NAG, 83G |
| 4 | 601 | 0.81 | 0.86 | 64 | NAG, 83G |
| 5 | 486 | 0.80 | 0.86 | 60 | NAG, 83G |
Interfaces
13 interfaces between chains.
- B–A · 2678 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 2592 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2581 Ų buried · 14 hydrogen bonds · protein-protein
- B–F · 908 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 874 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 70 glycan, 30 disulfide (N-glycosylation, disulfide).
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 P19550
- Every structure of UniProt B0FDK7
- Elsewhere: RCSB PDB 8FAD · PDBe 8FAD · UniProt P19550 · UniProt B0FDK7
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