MolNFT v1 · #187563 · protein
Sub-tomogram averaged structure of HIV-1 envelope protein in native membrane
7SKA · Envelope glycoprotein GP120: “Sub-tomogram averaged structure of HIV-1 envelope protein in native membrane”. Electron microscopy, 5 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.87). MolNFT v1 #187563 on GenesisL1: 3D…
- PDB
- 7SKA
- Type
- protein
- Length
- 1,788 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP120; Envelope glycoprotein GP41
- UniProt
- Q6TAN8
- Ligands
- NAG, MAN, BMA, FUC, GAL
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 2 distinct chains · 21% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, N, Y | Envelope glycoprotein GP120 | protein | 454 | 12% helix, 25% strand | Q6TAN8 |
| B, O, Z | Envelope glycoprotein GP41 | protein | 142 | 50% helix, 5% strand | Q6TAN8 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 117 copies · chains A, B, N, O, Y, Z
- MAN · alpha-D-mannopyranose · sugar · 45 copies
- BMA · beta-D-mannopyranose · sugar · 30 copies · chains A, N, Y
- FUC · alpha-L-fucopyranose · sugar · 6 copies · chains B, O, Z
- GAL · beta-D-galactopyranose · sugar · 6 copies
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 | 604 | 0.87 | 0.92 | 75 | empty |
| 2 | 188 | 0.82 | 0.96 | 40 | empty |
| 3 | 192 | 0.82 | 0.96 | 37 | empty |
| 4 | 213 | 0.81 | 0.94 | 43 | empty |
| 5 | 177 | 0.81 | 0.96 | 44 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3083 Ų buried · 36 hydrogen bonds · protein-protein
- N–O · 3082 Ų buried · 35 hydrogen bonds · protein-protein
- Y–Z · 3077 Ų buried · 36 hydrogen bonds · protein-protein
- B–Z · 536 Ų buried · 8 hydrogen bonds · protein-protein
- B–O · 534 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide (disulfide).
Compared structures
- 7SKA · Sub-tomogram averaged structure of HIV-1 Envelope protein in native membrane · 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 Q6TAN8
- Elsewhere: RCSB PDB 7SKA · PDBe 7SKA · UniProt Q6TAN8
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