MolNFT v1 · #112454 · protein
Crystal structure of the ornithine aminotransferase from toxoplasma gondii ME49 in a complex with the schiff base between plp and LYS286
4ZLV · Ornithine aminotransferase, mitochondrial, putative: “Crystal structure of the ornithine aminotransferase from toxoplasma gondii ME49 in a complex with the schiff…”. X-ray diffraction, 2 ligands (PLP, SO4), 5 pockets (best…
- PDB
- 4ZLV
- Type
- protein
- Length
- 843 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ornithine aminotransferase, mitochondrial, putative
- EC
- 2.6.1.13
- UniProt
- S8EY38
- Ligands
- PLP, SO4
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ornithine aminotransferase, mitochondrial, putative (EC 2.6.1.13) | protein | 421 | 41% helix, 19% strand | S8EY38 |
| B | Ornithine aminotransferase, mitochondrial, putative (EC 2.6.1.13) | protein | 422 | 41% helix, 19% strand | S8EY38 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains 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 | 397 | 0.76 | 0.86 | 58 | PLP |
| 2 | 91 | 0.73 | 0.96 | 31 | PLP |
| 3 | 367 | 0.68 | 0.81 | 41 | empty |
| 4 | 82 | 0.54 | 0.85 | 23 | empty |
| 5 | 66 | 0.54 | 0.87 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 5957 Ų buried · 86 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 1 disulfide (pyridoxal phosphate Schiff base, disulfide).
Compared structures
- 4ZLV · 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 4ZLV · PDBe 4ZLV · UniProt S8EY38
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