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Crystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49 in a complex with gabaculine
Analyse Crystal structure of the ornithine aminotransferase from Toxoplasma gondii ME49… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DJ9
- Type
- protein
- Length
- 842 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.55
- Source
- Toxoplasma gondii ME49
- Molecule
- Ornithine aminotransferase, mitochondrial
- EC
- 2.6.1.13
- UniProt
- S8EY38
- Ligands
- PXG, SO4
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · resolution 1.55 · 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, 19% strand | S8EY38 |
Ligands and binding sites
- PXG · 3-[O-phosphonopyridoxyl]--amino-benzoic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 469 | 0.79 | 0.87 | 65 | PXG |
| 2 | 432 | 0.77 | 0.86 | 58 | PXG |
| 3 | 67 | 0.59 | 0.90 | 19 | empty |
| 4 | 94 | 0.58 | 0.86 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 5909 Ų buried · 85 hydrogen bonds · protein-protein
Compared structures
- 5DJ9 · Crystal structure of the ornithine aminotransferase from toxoplasma gondii ME49 in a… · 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 5DJ9 · PDBe 5DJ9 · UniProt S8EY38
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