Research workbench
BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAbC-5 from animal Rh.33311 (Wk26 time point)
Analyse BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAbC-5 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L8Y
- Type
- protein
- Length
- 1,951 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.2
- Source
- Human immunodeficiency virus 1; Macaca mulatta
- Molecule
- Rh.33311 pAbC-5 - Heavy Chain; Rh.33311 pAbC-5 - Light Chain; BG505 SOSIP.v5.2 N241/N289…
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · resolution 4.2 · 8 distinct chains · 25% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Rh.33311 pAbC-5 - Heavy Chain | protein | 113 | 0% helix, 35% strand | — |
| L | Rh.33311 pAbC-5 - Light Chain | protein | 99 | 9% helix, 23% strand | — |
| C | BG505 SOSIP.v5.2 N241/N289 - gp120 | protein | 437 | 14% helix, 44% strand | — |
| D | BG505 SOSIP.v5.2 N241/N289 - gp41 | protein | 142 | 67% helix, 6% strand | — |
| A | BG505 SOSIP.v5.2 N241/N289 - gp120 | protein | 439 | 14% helix, 44% strand | — |
| B | BG505 SOSIP.v5.2 N241/N289 - gp41 | protein | 143 | 67% helix, 6% strand | — |
| E | BG505 SOSIP.v5.2 N241/N289 - gp120 | protein | 435 | 14% helix, 43% strand | — |
| F | BG505 SOSIP.v5.2 N241/N289 - gp41 | protein | 143 | 71% helix, 5% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 71 copies · chains C, A, E, D, B, H, L, F
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains C, A, 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 799 | 0.84 | 0.87 | 104 | empty |
| 2 | 822 | 0.80 | 0.83 | 85 | empty |
| 3 | 822 | 0.80 | 0.82 | 90 | empty |
| 4 | 501 | 0.78 | 0.85 | 61 | empty |
| 5 | 823 | 0.77 | 0.81 | 96 | empty |
Interfaces
17 interfaces between chains.
- A–B · 2692 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 2616 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2594 Ų buried · 18 hydrogen bonds · protein-protein
- B–F · 1197 Ų buried · 4 hydrogen bonds · protein-protein
- D–B · 1182 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 58 glycan, 35 disulfide (N-glycosylation, disulfide).
Compared structures
- 7L8Y · BG505 SOSIP.V5.2 N241/N289 in complex with the polyclonal Fab pabc-5 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 7L8Y · PDBe 7L8Y
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