Research workbench
Structure of ornithine aminotransferase triple mutant Y85I Y55A G320F
Analyse Structure of ornithine aminotransferase triple mutant Y85I Y55A G320F in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BYL
- Type
- protein
- Length
- 1,212 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ornithine aminotransferase
- EC
- 2.6.1.13
- UniProt
- P04181
- Ligands
- PLP
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 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
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 387 | 0.76 | 0.86 | 63 | PLP |
| 2 | 425 | 0.76 | 0.85 | 60 | PLP |
| 3 | 822 | 0.73 | 0.78 | 59 | empty |
| 4 | 61 | 0.46 | 0.84 | 15 | empty |
| 5 | 150 | 0.46 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5244 Ų buried · 65 hydrogen bonds · protein-protein
- B–C · 691 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 216 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2BYL · Structure of ornithine aminotransferase triple mutant Y85I Y55A G320F · the same entry in another collection · chain A against A, TM-score 1.00
- P04181 · AlphaFold monomer V2.0 prediction for ornithine aminotransferase, mitochondrial (P04181) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 2BYL · PDBe 2BYL · UniProt P04181
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