MolNFT v1 · #181088 · protein
Ornithine aminotransferase (oat) cocrystallized with its potent inhibitor - (S)-3-amino-4,4-difluorocyclopent-1-enecarboxylic acid (ss-1-148)
7LK0 · Ornithine aminotransferase, mitochondrial: “Ornithine aminotransferase (oat) cocrystallized with its potent inhibitor…”. X-ray diffraction, 1 ligand (Y3D), 11 pockets (best druggability 0.64). MolNFT v1 #181088 on GenesisL1: 3D…
- PDB
- 7LK0
- Type
- protein
- Length
- 1,207 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
- Y3D
- Pockets
- 11 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ornithine aminotransferase, mitochondrial (EC 2.6.1.13) | protein | 402 | 39% helix, 18% strand | P04181 |
| C | Ornithine aminotransferase, mitochondrial (EC 2.6.1.13) | protein | 403 | 38% helix, 18% strand | P04181 |
Ligands and binding sites
- Y3D · (1R,3S)-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy) methyl]pyridin-4-yl}methylidene)amino]-4-oxocyclopentane-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
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.64 | 0.76 | 54 | Y3D |
| 2 | 509 | 0.64 | 0.76 | 58 | Y3D |
| 3 | 335 | 0.60 | 0.77 | 34 | empty |
| 4 | 328 | 0.59 | 0.77 | 33 | empty |
| 5 | 321 | 0.55 | 0.75 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–B · 298 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 286 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 26 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7LK0 · Ornithine Aminotransferase (OAT) cocrystallized 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 7LK0 · PDBe 7LK0 · UniProt P04181
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