MolNFT v1 · #180721 · protein
BG505 SOSIP.V5.2 N241/N289 in complex with the polyclonal Fab pabc-8 from animal RH.33311 (WK26 time point)
7L90 · BG505 SOSIP.V5.2 N241/N289 - GP120: “BG505 SOSIP.V5.2 N241/N289 in complex with the polyclonal Fab pabc-8 from animal RH.33311 (WK26 time point)”. Electron microscopy, 3 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.81).…
- PDB
- 7L90
- Type
- protein
- Length
- 1,895 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-8…
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 7 distinct chains · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BG505 SOSIP.V5.2 N241/N289 - GP120 | protein | 436 | 16% helix, 43% strand | — |
| B, F | BG505 SOSIP.V5.2 N241/N289 - GP41 | protein | 129 | 62% helix, 5% strand | — |
| C | BG505 SOSIP.V5.2 N241/N289 - GP120 | protein | 436 | 17% helix, 43% strand | — |
| D | BG505 SOSIP.V5.2 N241/N289 - GP41 | protein | 127 | 65% helix, 7% strand | — |
| E | BG505 SOSIP.V5.2 N241/N289 - GP120 | protein | 437 | 16% helix, 41% strand | — |
| H | RH.33311 pabc-8 - heavy chain | protein | 108 | 3% helix, 10% strand | — |
| L | RH.33311 pabc-8 - light chain | protein | 93 | 0% helix, 6% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 72 copies · chains A, B, C, E, D, F
- BMA · beta-D-mannopyranose · sugar · 3 copies
- MAN · alpha-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 | 731 | 0.81 | 0.85 | 66 | empty |
| 2 | 510 | 0.77 | 0.84 | 62 | empty |
| 3 | 463 | 0.76 | 0.84 | 74 | empty |
| 4 | 523 | 0.74 | 0.82 | 64 | NAG |
| 5 | 59 | 0.74 | 0.98 | 21 | empty |
Interfaces
20 interfaces between chains.
- E–F · 2488 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 2478 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 2398 Ų buried · 18 hydrogen bonds · protein-protein
- D–F · 1119 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 1114 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 62 glycan, 33 disulfide (N-glycosylation, disulfide).
Compared structures
- 7L90 · BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAbC-8 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 7L90 · PDBe 7L90
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