MolNFT v1 · #159222 · protein
(1S,3S)-3-amino-4-(perfluoropropan-2-YLIDENE)CYCLOPENTANE-1-carboxylic acid hydrochloride, a potent inhibitor of ornithine aminotransferase
6OIA · Ornithine aminotransferase, mitochondrial: “(1S,3S)-3-amino-4-(perfluoropropan-2-YLIDENE)CYCLOPENTANE-1-carboxylic acid hydrochloride, a potent inhibitor…”. X-ray diffraction, 2 ligands (PLP, MQ4), 7 pockets (best druggability…
- PDB
- 6OIA
- Type
- protein
- Length
- 1,212 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, MQ4
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Ornithine aminotransferase, mitochondrial (EC 2.6.1.13) | protein | 404 | 38% helix, 20% strand | P04181 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 3 copies · chains A, B, C
- MQ4 · (1S)-3-amino-4-[(2S)-1,1,1-trifluoro-3-oxopropan-2-yl]cyclopent-3-ene-1-carboxylic acid · ligand · 2 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.78 | 0.86 | 56 | PLP, MQ4 |
| 2 | 405 | 0.76 | 0.85 | 56 | PLP |
| 3 | 768 | 0.72 | 0.78 | 53 | GOL |
| 4 | 262 | 0.56 | 0.77 | 38 | PLP, MQ4 |
| 5 | 286 | 0.55 | 0.76 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5301 Ų buried · 76 hydrogen bonds · protein-protein
- B–C · 677 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 220 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6OIA · (1S,3S)-3-amino-4-(perfluoropropan-2-ylidene)cyclopentane-1-carboxylic acid… · 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 6OIA · PDBe 6OIA · UniProt P04181
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.