Research workbench
Complex structure of FAB35 and mouse nachr ALPHA1
Analyse Complex structure of FAB35 and mouse nachr ALPHA1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HBV
- Type
- protein
- Length
- 716 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-bungarotoxin isoform V31; Acetylcholine receptor subunit alpha 1; FAB35, light…
- UniProt
- P60616, P04756
- Ligands
- MAN, NAG, BMA
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-bungarotoxin isoform V31 | protein | 74 | 5% helix, 36% strand | P60616 |
| B | Acetylcholine receptor subunit alpha 1 | protein | 212 | 9% helix, 53% strand | P04756 |
| C | FAB35, light chain | protein | 211 | 6% helix, 50% strand | — |
| D | FAB35, heavy chain | protein | 219 | 6% helix, 52% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
- BMA · beta-D-mannopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 597 | 0.64 | 0.75 | 55 | empty |
| 2 | 250 | 0.53 | 0.76 | 28 | empty |
| 3 | 95 | 0.38 | 0.76 | 20 | empty |
| 4 | 62 | 0.33 | 0.77 | 14 | empty |
| 5 | 73 | 0.32 | 0.74 | 21 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1791 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 771 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 691 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 323 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5HBV · Complex structure of Fab35 and mouse nAChR alpha1 · the same entry in another collection · chain A against A, TM-score 1.00
- P60616 · AlphaFold monomer V2.0 prediction for alpha-bungarotoxin isoform V31 (P60616) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P04756 · AlphaFold monomer V2.0 prediction for acetylcholine receptor subunit alpha (P04756) · a predicted model of the same protein · chain B against A, TM-score 0.94
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P60616
- Every structure of UniProt P04756
- Elsewhere: RCSB PDB 5HBV · PDBe 5HBV · UniProt P60616 · UniProt P04756
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