Research workbench
BG505 SOSIP.V5.2 N241/N289 in complex with the polyclonal Fab pabc-7 from animal RH.33311 (WK26 time point)
Analyse BG505 SOSIP.V5.2 N241/N289 in complex with the polyclonal Fab pabc-7 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L8Z
- Type
- protein
- Length
- 1,928 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RH.33311 pabc-7 - heavy chain; RH.33311 pabc-7 - light chain; BG505 SOSIP.V5.2 N241/N289…
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 8 distinct chains · 24% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | RH.33311 pabc-7 - heavy chain | protein | 109 | 3% helix, 37% strand | — |
| L | RH.33311 pabc-7 - light chain | protein | 85 | 0% helix, 22% strand | — |
| A | BG505 SOSIP.V5.2 N241/N289 - GP120 | protein | 445 | 16% helix, 42% strand | — |
| B | BG505 SOSIP.V5.2 N241/N289 - GP41 | protein | 136 | 61% helix, 5% strand | — |
| C | BG505 SOSIP.V5.2 N241/N289 - GP120 | protein | 446 | 16% helix, 43% strand | — |
| E | BG505 SOSIP.V5.2 N241/N289 - GP41 | protein | 134 | 66% helix, 2% strand | — |
| D | BG505 SOSIP.V5.2 N241/N289 - GP120 | protein | 436 | 14% helix, 42% strand | — |
| F | BG505 SOSIP.V5.2 N241/N289 - GP41 | protein | 137 | 63% helix, 5% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 83 copies · chains A, D, C, E, B, F
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, C, D
- BMA · beta-D-mannopyranose · sugar · 4 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 | 418 | 0.83 | 0.91 | 54 | empty |
| 2 | 427 | 0.81 | 0.88 | 64 | empty |
| 3 | 349 | 0.79 | 0.89 | 45 | empty |
| 4 | 663 | 0.73 | 0.80 | 81 | empty |
| 5 | 855 | 0.73 | 0.78 | 78 | empty |
Interfaces
18 interfaces between chains.
- C–E · 2639 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2528 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 2484 Ų buried · 20 hydrogen bonds · protein-protein
- B–E · 1307 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 1222 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 61 glycan, 33 disulfide (N-glycosylation, disulfide).
Compared structures
- 7L8Z · BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAbC-7 from animal Rh.33311… · the same entry in another collection · chain H against H, 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 7L8Z · PDBe 7L8Z
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