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Human ornithine aminotransferase cocrystallized with its inhibitor, (S,E)-3-amino-4-(FLUOROMETHYLENE)CYCLOPENT-1-ene-1-carboxylate
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
- 7TED
- Type
- protein
- Length
- 3,636 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ornithine aminotransferase, mitochondrial
- EC
- 2.6.1.13
- UniProt
- P04181
- Ligands
- I1T, PLP
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I | Ornithine aminotransferase, mitochondrial (EC 2.6.1.13) | protein | 404 | 38% helix, 19% strand | P04181 |
Ligands and binding sites
- I1T · (1S,3R,4S)-3-formyl-4-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl) amino]cyclopentane-1-carboxylic acid · ligand · 8 copies · chains A, B, C, I, D, E, F, G, H
- PLP · Pyridoxal-5'-phosphate · ligand · chains C, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 405 | 0.78 | 0.88 | 63 | I1T |
| 2 | 408 | 0.78 | 0.87 | 54 | I1T |
| 3 | 997 | 0.78 | 0.80 | 71 | empty |
| 4 | 417 | 0.77 | 0.86 | 59 | PLP |
| 5 | 401 | 0.76 | 0.86 | 54 | I1T |
Interfaces
16 interfaces between chains.
- C–I · 5429 Ų buried · 85 hydrogen bonds · protein-protein
- A–B · 5392 Ų buried · 82 hydrogen bonds · protein-protein
- B–C · 704 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 594 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 514 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7TED · Human Ornithine Aminotransferase cocrystallized with its inhibitor… · the same entry in another collection · chain I against I, 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 0.99
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 7TED · PDBe 7TED · UniProt P04181
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