MolNFT v1 · #167539 · protein
BG505 SOSIP.V5.2 in complex with rabbit Fab 43A2
6VO0 · 43A2 light chain: “BG505 SOSIP.V5.2 in complex with rabbit Fab 43A2”. Electron microscopy, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.83). MolNFT v1 #167539 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VO0
- Type
- protein
- Length
- 2,364 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 43A2 light chain; 43A2 heavy chain; Envelope glycoprotein GP120; Envelope glycoprotein…
- UniProt
- Q2N0S6
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 19% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, J, K | 43A2 light chain | protein | 113 | 5% helix, 50% strand | — |
| H, G, I | 43A2 heavy chain | protein | 120 | 5% helix, 49% strand | — |
| A, C, D | Envelope glycoprotein GP120 | protein | 433 | 15% helix, 42% strand | Q2N0S6 |
| B, E, F | Envelope glycoprotein GP41 | protein | 122 | 62% helix, 5% strand | Q2N0S6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 69 copies · chains H, A, L, G, C, J, I, D, K, B, E, F
- BMA · beta-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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 470 | 0.83 | 0.90 | 61 | empty |
| 2 | 371 | 0.75 | 0.85 | 51 | NAG |
| 3 | 387 | 0.73 | 0.84 | 52 | NAG |
| 4 | 395 | 0.73 | 0.84 | 51 | NAG |
| 5 | 418 | 0.69 | 0.80 | 57 | empty |
Interfaces
21 interfaces between chains.
- A–B · 2379 Ų buried · 16 hydrogen bonds · protein-protein
- C–E · 2377 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 2372 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1021 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 1018 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 42 disulfide (N-glycosylation, disulfide).
Compared structures
- 6VO0 · BG505 SOSIP.v5.2 in complex with rabbit Fab 43A2 · the same entry in another collection · chain L against L, 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 6VO0 · PDBe 6VO0 · UniProt Q2N0S6
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