Research workbench
Crystal structure of a putative ornithine aminotransferase from toxoplasma gondii ME49 in complex with pyrodoxal-5'-phosphate
Analyse Crystal structure of a putative ornithine aminotransferase from toxoplasma… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NOG
- Type
- protein
- Length
- 846 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative ornithine aminotransferase, mitochondrial
- EC
- 2.6.1.13
- UniProt
- S8EY38
- Ligands
- PLP
- 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 | Putative ornithine aminotransferase, mitochondrial (EC 2.6.1.13) | protein | 422 | 41% helix, 18% strand | S8EY38 |
| B | Putative ornithine aminotransferase, mitochondrial (EC 2.6.1.13) | protein | 424 | 41% helix, 18% strand | S8EY38 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains B
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 455 | 0.78 | 0.86 | 58 | PLP |
| 2 | 472 | 0.77 | 0.85 | 61 | PLP |
| 3 | 121 | 0.60 | 0.86 | 24 | empty |
| 4 | 81 | 0.55 | 0.86 | 29 | empty |
| 5 | 51 | 0.26 | 0.74 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 5971 Ų buried · 85 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 disulfide (additive adduct, disulfide).
Compared structures
- 4NOG · Crystal structure of a putative ornithine aminotransferase from Toxoplasma gondii ME49 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 4NOG · PDBe 4NOG · UniProt S8EY38
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