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Structure of the ornithine aminotransferase from toxoplasma gondii crystallized in presence of oxidized glutathione reveals partial occupancy of plp at the protein active site
Analyse Structure of the ornithine aminotransferase from toxoplasma gondii crystallized… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EQC
- Type
- protein
- Length
- 848 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
- PLP, BGC, GLC
- Pockets
- 4 · best druggability 0.77
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 | 426 | 41% helix, 18% strand | S8EY38 |
| B | Ornithine aminotransferase, mitochondrial (EC 2.6.1.13) | protein | 422 | 41% helix, 18% strand | S8EY38 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · chains A
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains B
- BME · Beta-mercaptoethanol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.77 | 0.86 | 58 | PEG, PLP |
| 2 | 444 | 0.76 | 0.85 | 56 | PEG, PLP |
| 3 | 76 | 0.61 | 0.90 | 28 | empty |
| 4 | 105 | 0.50 | 0.82 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 6120 Ų buried · 89 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 5EQC · Structure of the ornithine aminotransferase from Toxoplasma gondii crystallized in… · 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 5EQC · PDBe 5EQC · UniProt S8EY38
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