Research workbench
Crystal structure of a plp-dependent enzyme
Analyse Crystal structure of a plp-dependent enzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1O69
- Type
- protein
- Length
- 742 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminotransferase
- UniProt
- Q9S5Y7
- Ligands
- X04
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminotransferase | protein | 374 | 40% helix, 18% strand | Q9S5Y7 |
| B | Aminotransferase | protein | 368 | 42% helix, 18% strand | Q9S5Y7 |
Ligands and binding sites
- X04 · (2-amino-4-formyl-5-hydroxy-6-methylpyridin-3-yl)methyl dihydrogen phosphate · ligand · 2 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1007 | 0.82 | 0.83 | 137 | X04 |
| 2 | 74 | 0.31 | 0.74 | 12 | BME |
| 3 | 52 | 0.24 | 0.72 | 10 | BME |
Interfaces
1 interface between chains.
- A–B · 2493 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (additive adduct, covalent ligand).
Compared structures
- 1O69 · Crystal structure of a PLP-dependent enzyme · 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 Q9S5Y7
- Elsewhere: RCSB PDB 1O69 · PDBe 1O69 · UniProt Q9S5Y7
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