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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
- 5J67
- Type
- protein
- Length
- 2,237 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.16
- Source
- Homo sapiens
- Molecule
- Astrotactin-2
- UniProt
- O75129
- Ligands
- I3P, MAN, NAG, BMA
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · resolution 3.16 · 4 distinct chains · 28% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Astrotactin-2 | protein | 559 | 28% helix, 29% strand | O75129 |
| B | Astrotactin-2 | protein | 558 | 28% helix, 29% strand | O75129 |
| C | Astrotactin-2 | protein | 563 | 28% helix, 28% strand | O75129 |
| D | Astrotactin-2 | protein | 557 | 28% helix, 29% strand | O75129 |
Ligands and binding sites
- I3P · D-myo-inositol-1,4,5-triphosphate · ligand · 4 copies · chains A, B, D, C
- MAN · alpha-D-mannopyranose · sugar · 28 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1192 | 0.71 | 0.75 | 105 | empty |
| 2 | 900 | 0.71 | 0.76 | 89 | empty |
| 3 | 786 | 0.70 | 0.77 | 75 | empty |
| 4 | 379 | 0.64 | 0.79 | 54 | empty |
| 5 | 382 | 0.63 | 0.78 | 40 | I3P |
Interfaces
4 interfaces between chains.
- B–D · 939 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 876 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 472 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 381 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 5J67 · Structure of astrotactin-2, a conserved vertebrate-specific and perforin-like membrane… · the same entry in another collection · chain D against D, TM-score 1.00
- O75129 · AlphaFold monomer V2.0 prediction for astrotactin-2 (O75129) · a predicted model of the same protein · chain C 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 5J67 · PDBe 5J67 · UniProt O75129
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