Research workbench
BG505 SOSIP.V5.2 N241/N289 in complex with the polyclonal Fab pabc-2 from animal RH.33311 (WK26 time point)
Analyse BG505 SOSIP.V5.2 N241/N289 in complex with the polyclonal Fab pabc-2 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L8U
- Type
- protein
- Length
- 1,893 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-2…
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 8 distinct chains · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | BG505 SOSIP.V5.2 N241/N289 - GP120 | protein | 430 | 15% helix, 42% strand | — |
| D | BG505 SOSIP.V5.2 N241/N289 - GP41 | protein | 132 | 59% helix, 5% strand | — |
| A | BG505 SOSIP.V5.2 N241/N289 - GP120 | protein | 438 | 13% helix, 41% strand | — |
| B | BG505 SOSIP.V5.2 N241/N289 - GP41 | protein | 126 | 53% helix, 2% strand | — |
| E | BG505 SOSIP.V5.2 N241/N289 - GP120 | protein | 431 | 15% helix, 43% strand | — |
| F | BG505 SOSIP.V5.2 N241/N289 - GP41 | protein | 118 | 61% helix, 6% strand | — |
| H | RH.33311 pabc-2 - heavy chain | protein | 113 | 3% helix, 36% strand | — |
| L | RH.33311 pabc-2 - light chain | protein | 105 | 0% helix, 30% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 71 copies · chains C, A, B, H, E, F
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, H, 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 | 674 | 0.81 | 0.85 | 63 | empty |
| 2 | 776 | 0.79 | 0.83 | 91 | empty |
| 3 | 1071 | 0.76 | 0.78 | 107 | empty |
| 4 | 793 | 0.76 | 0.80 | 86 | empty |
| 5 | 609 | 0.75 | 0.82 | 80 | empty |
Interfaces
15 interfaces between chains.
- A–B · 2400 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2330 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 2132 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 1028 Ų buried · 10 hydrogen bonds · protein-protein
- D–B · 930 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 59 glycan, 33 disulfide (N-glycosylation, disulfide).
Compared structures
- 7L8U · BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAbC-2 from animal Rh.33311… · the same entry in another collection · chain C against C, 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 7L8U · PDBe 7L8U
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.