MolNFT v1 · #181089 · protein
Ornithine aminotransferase (oat) with its potent inhibitor - (S)-3- amino-4,4-difluorocyclopent-1-enecarboxylic acid (ss-1-148) - 1 hour soaking
7LK1 · Ornithine aminotransferase, mitochondrial: “Ornithine aminotransferase (oat) with its potent inhibitor - (S)-3…”. X-ray diffraction, 1 ligand (Y37), 12 pockets (best druggability 0.70). MolNFT v1 #181089 on GenesisL1: 3D structure…
- PDB
- 7LK1
- Type
- protein
- Length
- 1,211 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
- Y37
- Pockets
- 12 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ornithine aminotransferase, mitochondrial (EC 2.6.1.13) | protein | 404 | 39% helix, 18% strand | P04181 |
| B | Ornithine aminotransferase, mitochondrial (EC 2.6.1.13) | protein | 403 | 39% helix, 18% strand | P04181 |
Ligands and binding sites
- Y37 · (1R,4R)-4-fluoro-3-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl) amino]cyclopent-2-ene-1-carboxylic acid · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.70 | 0.77 | 59 | empty |
| 2 | 558 | 0.65 | 0.76 | 70 | Y37 |
| 3 | 528 | 0.64 | 0.76 | 49 | empty |
| 4 | 501 | 0.62 | 0.75 | 59 | Y37 |
| 5 | 511 | 0.62 | 0.75 | 60 | Y37 |
Interfaces
2 interfaces between chains.
- A–C · 632 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 490 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 7LK1 · Ornithine Aminotransferase (OAT) with its potent 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 7LK1 · PDBe 7LK1 · UniProt P04181
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