MolNFT v1 · #167039 · protein
VRC01 bound BG505 F14 HIV-1 sosip envelope trimer structure
6V8X · Envelope glycoprotein GP120: “VRC01 bound BG505 F14 HIV-1 sosip envelope trimer structure”. Electron microscopy, 3 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.82). MolNFT v1 #167039 on GenesisL1: 3D structure, binding…
- PDB
- 6V8X
- Type
- protein
- Length
- 2,997 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP120; Envelope glycoprotein GP41; VRC01 Fab heavy chain; VRC01 Fab…
- UniProt
- Q2N0S6, Q2N0S9, Q6N095, Q6PIL8
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 13% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I | Envelope glycoprotein GP120 | protein | 439 | 9% helix, 37% strand | Q2N0S6 |
| B, F, J | Envelope glycoprotein GP41 | protein | 128 | 59% helix, 5% strand | Q2N0S9 |
| C, G, K | VRC01 Fab heavy chain | protein | 224 | 4% helix, 35% strand | Q6N095 |
| D, H, L | VRC01 Fab light chain | protein | 208 | 3% helix, 33% strand | Q6PIL8 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 87 copies · chains A, D, C, I, B, E, H, G, F, L, K, J
- BMA · beta-D-mannopyranose · sugar · 15 copies · chains D, H, L
- MAN · alpha-D-mannopyranose · sugar · 3 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 | 415 | 0.82 | 0.90 | 48 | empty |
| 2 | 694 | 0.78 | 0.83 | 91 | NAG |
| 3 | 155 | 0.74 | 0.92 | 25 | empty |
| 4 | 162 | 0.73 | 0.91 | 26 | empty |
| 5 | 66 | 0.72 | 0.97 | 20 | empty |
Interfaces
24 interfaces between chains.
- E–F · 2730 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2728 Ų buried · 22 hydrogen bonds · protein-protein
- I–J · 2720 Ų buried · 22 hydrogen bonds · protein-protein
- K–L · 2210 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 2208 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 disulfide, 51 glycan (disulfide, N-glycosylation).
Compared structures
- 6V8X · VRC01 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure · 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
- Every structure of UniProt Q2N0S9
- Every structure of UniProt Q6N095
- Every structure of UniProt Q6PIL8
- Elsewhere: RCSB PDB 6V8X · PDBe 6V8X · UniProt Q2N0S6 · UniProt Q2N0S9 · UniProt Q6N095 · UniProt Q6PIL8
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