Research workbench
Crystal structure of human pyridoxine 5'-phosphate oxidase R229W mutant
Analyse Crystal structure of human pyridoxine 5'-phosphate oxidase R229W mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HY8
- Type
- protein
- Length
- 211 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxine-5'-phosphate oxidase
- EC
- 1.4.3.5
- UniProt
- Q9NVS9
- Ligands
- FMN, PLP, PO4
- Pockets
- 1 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxine-5'-phosphate oxidase (EC 1.4.3.5) | protein | 211 | 26% helix, 31% strand | Q9NVS9 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- PO4 · Phosphate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.47 | 0.76 | 21 | empty |
Compared structures
- 3HY8 · Crystal Structure of Human Pyridoxine 5'-Phosphate Oxidase R229W Mutant · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NVS9 · AlphaFold monomer V2.0 prediction for pyridoxine-5'-phosphate oxidase (Q9NVS9) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9NVS9
- Elsewhere: RCSB PDB 3HY8 · PDBe 3HY8 · UniProt Q9NVS9
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