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Structure of the ornithine aminotransferase from toxoplasma gondii in complex with inactivator
Analyse Structure of the ornithine aminotransferase from toxoplasma gondii in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E5I
- Type
- protein
- Length
- 842 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ornithine aminotransferase, mitochondrial
- EC
- 2.6.1.13
- UniProt
- S8EY38
- Ligands
- 5NJ, 5JV, SO4
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ornithine aminotransferase, mitochondrial (EC 2.6.1.13) | protein | 421 | 41% helix, 18% strand | S8EY38 |
| B | Ornithine aminotransferase, mitochondrial (EC 2.6.1.13) | protein | 421 | 41% helix, 18% strand | S8EY38 |
Ligands and binding sites
- 5NJ · 6-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]-4-oxidanylidene-hexanoic acid · ligand · chains A, B
- 5JV · 4-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]pent-4-enoic acid · ligand · chains A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 484 | 0.78 | 0.85 | 69 | 5JV |
| 2 | 96 | 0.75 | 0.96 | 34 | 5NJ |
| 3 | 388 | 0.69 | 0.81 | 44 | empty |
| 4 | 117 | 0.61 | 0.87 | 21 | empty |
| 5 | 101 | 0.59 | 0.86 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 6027 Ų buried · 92 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 5E5I · Structure of the ornithine aminotransferase from Toxoplasma gondii in complex with… · the same entry in another collection · 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 S8EY38
- Elsewhere: RCSB PDB 5E5I · PDBe 5E5I · UniProt S8EY38
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