MolNFT v1 · #175325 · protein
2,5-dihydroxypridine dioxygenase in complex with 2,5-dihydroxypridine and product N-formylmaleamic acid
7CN3 · 2,5-dihydroxypyridine 5,6-dioxygenase: “2,5-dihydroxypridine dioxygenase in complex with 2,5-dihydroxypridine and product N-formylmaleamic acid”. X-ray diffraction, 3 ligands (G6C, D6O, FE2), 20 pockets (best druggability 0.87).…
- PDB
- 7CN3
- Type
- protein
- Length
- 2,090 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,5-dihydroxypyridine 5,6-dioxygenase
- EC
- 1.13.11.9
- UniProt
- Q88FY1
- Ligands
- G6C, D6O, FE2
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F | 2,5-dihydroxypyridine 5,6-dioxygenase (EC 1.13.11.9) | protein | 348 | 29% helix, 28% strand | Q88FY1 |
| C, D | 2,5-dihydroxypyridine 5,6-dioxygenase (EC 1.13.11.9) | protein | 349 | 28% helix, 28% strand | Q88FY1 |
Ligands and binding sites
- G6C · 5-oxidanyl-1H-pyridin-2-one · ligand · 4 copies · chains C, D, E, F
- D6O · (~{Z})-4-formamido-4-oxidanylidene-but-2-enoic acid · ligand · 2 copies · chains A, B
- FE2 · Fe (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, C, D, E, F
- PGE · Triethylene glycol · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 763 | 0.87 | 0.91 | 86 | empty |
| 2 | 740 | 0.87 | 0.91 | 90 | empty |
| 3 | 983 | 0.83 | 0.84 | 133 | empty |
| 4 | 437 | 0.79 | 0.87 | 68 | G6C |
| 5 | 390 | 0.74 | 0.84 | 50 | D6O |
Interfaces
12 interfaces between chains.
- A–F · 1196 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1191 Ų buried · 21 hydrogen bonds · protein-protein
- B–E · 1184 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1184 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1173 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 7CN3 · 2,5-dihydroxypridine Dioxygenase in complex with 2,5-dihydroxypridine and product… · the same entry in another collection · chain F against F, TM-score 1.00
- Q88FY1 · AlphaFold monomer V2.0 prediction for 2,5-dihydroxypyridine 5,6-dioxygenase (Q88FY1) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q88FY1
- Elsewhere: RCSB PDB 7CN3 · PDBe 7CN3 · UniProt Q88FY1
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