Research workbench
Ornithine aminotransferase mutant Y85I
Analyse Ornithine aminotransferase mutant Y85I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BYJ
- Type
- protein
- Length
- 1,212 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.02
- Source
- HOMO SAPIENS
- Molecule
- Ornithine aminotransferase
- EC
- 2.6.1.13
- UniProt
- P04181
- Ligands
- PLP
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · resolution 3.02 · 1 distinct chain · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Ornithine aminotransferase (EC 2.6.1.13) | protein | 404 | 39% helix, 20% strand | P04181 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 491 | 0.77 | 0.85 | 62 | PLP |
| 2 | 479 | 0.76 | 0.84 | 60 | PLP |
| 3 | 843 | 0.73 | 0.78 | 65 | empty |
| 4 | 516 | 0.63 | 0.76 | 64 | PLP |
| 5 | 138 | 0.44 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5277 Ų buried · 73 hydrogen bonds · protein-protein
- B–C · 696 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 198 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor (pyridoxal phosphate Schiff base).
Compared structures
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 P04181
- Elsewhere: RCSB PDB 2BYJ · PDBe 2BYJ · UniProt P04181
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