MolNFT v1 · #180714 · protein
BG505 SOSIP.V5.2 N241/N289 in complex with the polyclonal Fab pabc-1 from animal RH.33311 (WK26 time point)
7L8T · BG505 SOSIP.V5.2 N241/N289 - GP120: “BG505 SOSIP.V5.2 N241/N289 in complex with the polyclonal Fab pabc-1 from animal RH.33311 (WK26 time point)”. Electron microscopy, 3 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.86).…
- PDB
- 7L8T
- Type
- protein
- Length
- 1,994 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BG505 SOSIP.V5.2 N241/N289 - GP120; BG505 SOSIP.V5.2 N241/N289 - GP41; RH.33311 pabc-1…
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 6 distinct chains · 24% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BG505 SOSIP.V5.2 N241/N289 - GP120 | protein | 446 | 14% helix, 39% strand | — |
| B | BG505 SOSIP.V5.2 N241/N289 - GP41 | protein | 152 | 68% helix, 7% strand | — |
| C, E | BG505 SOSIP.V5.2 N241/N289 - GP120 | protein | 445 | 15% helix, 40% strand | — |
| D, F | BG505 SOSIP.V5.2 N241/N289 - GP41 | protein | 144 | 72% helix, 5% strand | — |
| H | RH.33311 pabc-1 - heavy chain | protein | 116 | 0% helix, 42% strand | — |
| L | RH.33311 pabc-1 - light chain | protein | 102 | 0% helix, 40% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 78 copies · chains A, B, C, E, D, F
- MAN · alpha-D-mannopyranose · sugar · 7 copies · chains A, C, E
- 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 590 | 0.86 | 0.91 | 91 | empty |
| 2 | 420 | 0.84 | 0.91 | 70 | empty |
| 3 | 548 | 0.82 | 0.87 | 74 | empty |
| 4 | 768 | 0.79 | 0.83 | 87 | empty |
| 5 | 158 | 0.78 | 0.94 | 30 | empty |
Interfaces
19 interfaces between chains.
- E–F · 2753 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2712 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2645 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1234 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 1233 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 66 glycan, 36 disulfide (N-glycosylation, disulfide).
Compared structures
- 7L8T · BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAbC-1 from animal Rh.33311… · 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
- Elsewhere: RCSB PDB 7L8T · PDBe 7L8T
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