MolNFT v1 · #166786 · protein
BG505 SOSIP.664 trimer
6V0R · BG505 SOSIPV5.2 GP120: “BG505 SOSIP.664 trimer”. Electron microscopy, 4 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.83). MolNFT v1 #166786 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6V0R
- Type
- protein
- Length
- 1,704 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BG505 SOSIPV5.2 GP120; BG505 SOSIPV5.2 GP41
- UniProt
- Q2N0S6
- Ligands
- NAG, BMA, MAN, FUC
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 26% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | BG505 SOSIPV5.2 GP120 | protein | 439 | 14% helix, 43% strand | Q2N0S6 |
| B, E, F | BG505 SOSIPV5.2 GP41 | protein | 129 | 65% helix, 5% strand | Q2N0S6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 84 copies · chains A, B, C, E, D, F
- BMA · beta-D-mannopyranose · sugar · 9 copies
- MAN · alpha-D-mannopyranose · sugar · 9 copies · chains A, C, D
- FUC · alpha-L-fucopyranose · sugar · 6 copies · chains A, B, C, E, D, F
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 | 357 | 0.83 | 0.92 | 44 | empty |
| 2 | 611 | 0.70 | 0.78 | 80 | empty |
| 3 | 619 | 0.69 | 0.78 | 69 | empty |
| 4 | 633 | 0.69 | 0.77 | 77 | empty |
| 5 | 282 | 0.64 | 0.81 | 39 | NAG |
Interfaces
15 interfaces between chains.
- D–F · 2504 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2497 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 2497 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1224 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 1223 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 glycan, 30 disulfide (N-glycosylation, disulfide).
Compared structures
- 6V0R · BG505 SOSIP.664 Trimer · 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 Q2N0S6
- Elsewhere: RCSB PDB 6V0R · PDBe 6V0R · UniProt Q2N0S6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.