Research workbench
Structure of astrotactin-2, a conserved vertebrate-specific and perforin-like membrane protein involved in neuronal development
Analyse Structure of astrotactin-2, a conserved vertebrate-specific and perforin-like… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J68
- Type
- protein
- Length
- 559 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Astrotactin-2
- UniProt
- O75129
- Ligands
- I3P, MAN, NAG, BMA
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Astrotactin-2 | protein | 559 | 27% helix, 29% strand | O75129 |
Ligands and binding sites
- I3P · D-myo-inositol-1,4,5-triphosphate · ligand · chains A
- MAN · alpha-D-mannopyranose · sugar · 7 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- BMA · beta-D-mannopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.61 | 0.78 | 40 | empty |
| 2 | 114 | 0.48 | 0.80 | 19 | empty |
| 3 | 98 | 0.46 | 0.80 | 20 | empty |
| 4 | 76 | 0.37 | 0.77 | 19 | empty |
| 5 | 73 | 0.35 | 0.76 | 20 | NAG |
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5J68 · Structure of Astrotactin-2, a conserved vertebrate-specific and perforin-like membrane… · the same entry in another collection · chain A against A, TM-score 1.00
- O75129 · AlphaFold monomer V2.0 prediction for astrotactin-2 (O75129) · a predicted model of the same protein · chain A 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 O75129
- Elsewhere: RCSB PDB 5J68 · PDBe 5J68 · UniProt O75129
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