MolNFT v1 · #117288 · protein
Crystal structure of the ornithine aminotransferase from toxoplasma gondii ME49 in a complex with (S)-4-amino-5-fluoropentanoic acid
5E3K: “Crystal structure of the ornithine aminotransferase from toxoplasma gondii ME49 in a complex with…”. X-ray diffraction, 3 ligands (5JV, SO4, CO3), 5 pockets (best druggability 0.78). MolNFT v1 #117288 on GenesisL1: 3D structure…
- PDB
- 5E3K
- Type
- protein
- Length
- 846 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminotransferase
- EC
- 2.6.1.13
- UniProt
- S8EY38
- Ligands
- 5JV, SO4, CO3
- 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 | Aminotransferase (EC 2.6.1.13) | protein | 422 | 41% helix, 18% strand | S8EY38 |
| B | Aminotransferase (EC 2.6.1.13) | protein | 424 | 41% helix, 18% strand | S8EY38 |
Ligands and binding sites
- 5JV · 4-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]pent-4-enoic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
- CO3 · Carbonate ion · ion · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 512 | 0.78 | 0.85 | 69 | 5JV |
| 2 | 464 | 0.78 | 0.86 | 65 | 5JV |
| 3 | 118 | 0.60 | 0.86 | 23 | empty |
| 4 | 100 | 0.59 | 0.87 | 26 | empty |
| 5 | 68 | 0.32 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 5956 Ų buried · 86 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5E3K · 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 5E3K · PDBe 5E3K · UniProt S8EY38
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