Research workbench
Structure of uncleaved HIV-1 jr-fl env glycoprotein trimer in state U2 bound to small molecule HIV-1 entry inhibitor bms-378806
Analyse Structure of uncleaved HIV-1 jr-fl env glycoprotein trimer in state U2 bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N6W
- Type
- protein
- Length
- 1,771 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP160
- UniProt
- Q75760
- Ligands
- 83G, NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 3 distinct chains · 23% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein GP160 | protein | 591 | 23% helix, 21% strand | Q75760 |
| B | Envelope glycoprotein GP160 | protein | 595 | 24% helix, 22% strand | Q75760 |
| C | Envelope glycoprotein GP160 | protein | 585 | 22% helix, 25% strand | Q75760 |
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 A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 87 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar · 20 copies · chains B
- MAN · alpha-D-mannopyranose · sugar · 13 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1143 | 0.89 | 0.90 | 161 | empty |
| 2 | 878 | 0.87 | 0.88 | 107 | NAG, 83G |
| 3 | 482 | 0.85 | 0.92 | 69 | NAG |
| 4 | 317 | 0.85 | 0.95 | 62 | empty |
| 5 | 696 | 0.85 | 0.88 | 84 | 83G |
Interfaces
3 interfaces between chains.
- B–C · 1624 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1313 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1189 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 47 glycan, 28 disulfide (N-glycosylation, disulfide).
Compared structures
- 7N6W · Structure of uncleaved HIV-1 JR-FL Env glycoprotein trimer in state U2 bound to small… · 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 Q75760
- Elsewhere: RCSB PDB 7N6W · PDBe 7N6W · UniProt Q75760
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