MolNFT v1 · #96920 · protein
Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase, 5-pyridoxic acid bound form
4JY3: “Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase, 5-pyridoxic acid bound form”. X-ray diffraction, 2 ligands (FAD, 5PR), 6 pockets (best druggability 0.82). MolNFT v1 #96920 on GenesisL1: 3D structure…
- PDB
- 4JY3
- Type
- protein
- Length
- 740 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
- EC
- 1.14.12.4
- UniProt
- Q988D3
- Ligands
- FAD, 5PR
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (EC 1.14.12.4) | protein | 370 | 35% helix, 27% strand | Q988D3 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- 5PR · 5-hydroxy-4-(hydroxymethyl)-6-methylpyridine-3-carboxylic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 904 | 0.82 | 0.83 | 81 | FAD, BME, 5PR |
| 2 | 976 | 0.80 | 0.82 | 82 | FAD, BME, 5PR |
| 3 | 124 | 0.42 | 0.76 | 17 | empty |
| 4 | 96 | 0.40 | 0.76 | 16 | empty |
| 5 | 88 | 0.32 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 316 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 4JY3 · Crystal structure of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase, 5-pyridoxic… · 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 Q988D3
- Elsewhere: RCSB PDB 4JY3 · PDBe 4JY3 · UniProt Q988D3
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