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Ornithine aminotransferase (oat) cocrystallized with its inactivator - (1S,3S)-3-amino-4-(DIFLUOROMETHYLENE)CYCLOHEXENE-1-carboxylic acid
Analyse Ornithine aminotransferase (oat) cocrystallized with its inactivator… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LON
- Type
- protein
- Length
- 1,203 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
- THR, 7QP
- Pockets
- 16 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C | Ornithine aminotransferase, mitochondrial (EC 2.6.1.13) | protein | 401 | 39% helix, 18% strand | P04181 |
Ligands and binding sites
- THR · Threonine · ligand · 3 copies · chains B, A, C
- 7QP · (1R,3S,4R)-3-[({3-hydroxy-2-methyl-5-[(phosphonooxy) methyl]pyridin-4-yl}methyl)amino]-4-methylcyclohexane-1-carboxylic acid · ligand · 3 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 544 | 0.66 | 0.77 | 66 | THR, 7QP |
| 2 | 538 | 0.63 | 0.75 | 60 | empty |
| 3 | 317 | 0.58 | 0.77 | 34 | empty |
| 4 | 243 | 0.56 | 0.78 | 43 | THR, 7QP |
| 5 | 274 | 0.53 | 0.75 | 27 | empty |
Interfaces
3 interfaces between chains.
- B–C · 314 Ų buried · 5 hydrogen bonds · protein-protein
- B–A · 307 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 48 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 7LON · Ornithine Aminotransferase (OAT) cocrystallized with its inactivator… · the same entry in another collection · chain B against B, TM-score 1.00
- P04181 · AlphaFold monomer V2.0 prediction for ornithine aminotransferase, mitochondrial (P04181) · a predicted model of the same protein · chain C 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 7LON · PDBe 7LON · UniProt P04181
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