MolNFT v1 · #93444 · protein
Tetrameric form of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (mhpco)
4H2P: “Tetrameric form of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (mhpco)”. X-ray diffraction, 2 ligands (FAD, SO4), 18 pockets (best druggability 0.81). MolNFT v1 #93444 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4H2P
- Type
- protein
- Length
- 1,481 residues
- Chains
- 4
- 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, SO4
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 28% 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 | 371 | 35% helix, 28% strand | Q988D3 |
| C | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (EC 1.14.12.4) | protein | 370 | 35% helix, 29% strand | Q988D3 |
| D | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (EC 1.14.12.4) | protein | 369 | 34% helix, 29% strand | Q988D3 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 51 copies · chains A, C, B, D
- PEG · Di(hydroxyethyl)ether · additive · 22 copies · chains A, B, C, D
- BME · Beta-mercaptoethanol · additive · 4 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 2 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 930 | 0.81 | 0.83 | 84 | FAD, BME, SO4, PEG |
| 2 | 1002 | 0.81 | 0.82 | 92 | FAD, BME, SO4 |
| 3 | 938 | 0.81 | 0.82 | 90 | FAD, BME, EDO |
| 4 | 922 | 0.80 | 0.82 | 84 | FAD, BME, EDO |
| 5 | 108 | 0.79 | 0.98 | 20 | empty |
Interfaces
6 interfaces between chains.
- C–D · 902 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 888 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 323 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 323 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 63 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 covalent (additive adduct).
Compared structures
- 4H2P · Tetrameric form of 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (MHPCO) · 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 4H2P · PDBe 4H2P · UniProt Q988D3
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