MolNFT v1 · #142355 · protein
Mandelate oxidase mutant-Y128F with 5-deazariboflavin mononucleotide and phenylpyruvic acid
6A1P · 4-hydroxymandelate oxidase: “Mandelate oxidase mutant-Y128F with 5-deazariboflavin mononucleotide and phenylpyruvic acid”. X-ray diffraction, 3 ligands (9O9, PPY, MG), 3 pockets (best druggability 0.74). MolNFT v1 #142355 on…
- PDB
- 6A1P
- Type
- protein
- Length
- 332 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxymandelate oxidase
- EC
- 1.1.3.46
- UniProt
- O52792
- Ligands
- 9O9, PPY, MG
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxymandelate oxidase (EC 1.1.3.46) | protein | 332 | 45% helix, 14% strand | O52792 |
Ligands and binding sites
- 9O9 · 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-5-O-phosphono-D-ribitol · ligand · chains A
- PPY · 3-phenylpyruvic acid · ligand · chains A
- MG · Magnesium ion · metal · chains A
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 | 325 | 0.74 | 0.86 | 50 | 9O9, MG, PPY |
| 2 | 95 | 0.38 | 0.75 | 20 | empty |
| 3 | 84 | 0.34 | 0.74 | 18 | empty |
Compared structures
- 6A1P · Mandelate oxidase mutant-Y128F with 5-deazariboflavin mononucleotide and phenylpyruvic… · the same entry in another collection · chain A against A, TM-score 1.00
- O52792 · AlphaFold monomer V2.0 prediction for 4-hydroxymandelate oxidase (O52792) · a predicted model of the same protein · 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 O52792
- Elsewhere: RCSB PDB 6A1P · PDBe 6A1P · UniProt O52792
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