Research workbench
Crystal structure of neuronal leucine rich repeat protein amigo-1
Analyse Crystal structure of neuronal leucine rich repeat protein amigo-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XOT
- Type
- protein
- Length
- 664 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amphoterin-induced protein 1
- UniProt
- Q80ZD8
- Ligands
- NAG, BMA
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amphoterin-induced protein 1 | protein | 331 | 11% helix, 24% strand | Q80ZD8 |
| B | Amphoterin-induced protein 1 | protein | 333 | 12% helix, 23% strand | Q80ZD8 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 978 | 0.76 | 0.78 | 90 | empty |
| 2 | 260 | 0.50 | 0.74 | 30 | empty |
| 3 | 230 | 0.49 | 0.75 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1458 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 2XOT · Crystal structure of neuronal leucine rich repeat protein AMIGO-1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q80ZD8 · AlphaFold monomer V2.0 prediction for amphoterin-induced protein 1 (Q80ZD8) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q80ZD8
- Elsewhere: RCSB PDB 2XOT · PDBe 2XOT · UniProt Q80ZD8
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