MolNFT v1 · #26629 · protein
X-ray structure of escherichia COLI pyridoxine 5'-phosphate oxidase in tetragonal crystal form
1WV4 · Pyridoxamine 5'-phosphate oxidase: “X-ray structure of escherichia COLI pyridoxine 5'-phosphate oxidase in tetragonal crystal form”. X-ray diffraction, 2 ligands (FMN, PO4), 3 pockets (best druggability 0.62). MolNFT v1 #26629 on…
- PDB
- 1WV4
- Type
- protein
- Length
- 316 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxamine 5'-phosphate oxidase
- EC
- 1.4.3.5
- UniProt
- P28225
- Ligands
- FMN, PO4
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxamine 5'-phosphate oxidase (EC 1.4.3.5) | protein | 162 | 18% helix, 42% strand | P28225 |
| B | Pyridoxamine 5'-phosphate oxidase (EC 1.4.3.5) | protein | 154 | 18% helix, 44% strand | P28225 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.62 | 0.79 | 31 | FMN |
| 2 | 292 | 0.61 | 0.79 | 30 | FMN |
| 3 | 71 | 0.53 | 0.86 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1350 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1WV4 · X-ray Structure of Escherichia coli pyridoxine 5'-phosphate oxidase in tetragonal crystal… · 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 P28225
- Elsewhere: RCSB PDB 1WV4 · PDBe 1WV4 · UniProt P28225
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