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Human ornithine aminotransferase cocrystallized with its inhibitor, (1S,3S)-3-amino-4-(DIFLUOROMETHYLENE)CYCLOPENTANE-1-carboxylic acid.
Analyse Human ornithine aminotransferase cocrystallized with its inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TFP
- Type
- protein
- Length
- 1,206 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ornithine aminotransferase, mitochondrial
- EC
- 2.6.1.13
- UniProt
- P04181
- Ligands
- PLP, I2V
- Pockets
- 13 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Ornithine aminotransferase, mitochondrial (EC 2.6.1.13) | protein | 402 | 37% helix, 18% strand | P04181 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 3 copies · chains A, B, C
- I2V · (1S,3S,4S)-3-amino-4-(fluoromethyl)cyclopentane-1-carboxylic acid · ligand · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 651 | 0.70 | 0.78 | 58 | empty |
| 2 | 604 | 0.66 | 0.76 | 63 | PLP, I2V |
| 3 | 535 | 0.64 | 0.76 | 67 | PLP |
| 4 | 501 | 0.63 | 0.76 | 46 | empty |
| 5 | 489 | 0.62 | 0.76 | 56 | PLP |
Interfaces
2 interfaces between chains.
- A–C · 615 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 494 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 7TFP · Human Ornithine Aminotransferase cocrystallized with its inhibitor… · 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 7TFP · PDBe 7TFP · UniProt P04181
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