Research workbench
Structure of 2,5-dihydroxypridine dioxygenase from pseudomonas putida KT2440
Analyse Structure of 2,5-dihydroxypridine dioxygenase from pseudomonas putida KT2440 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CUP
- Type
- protein
- Length
- 2,086 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
- FE
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 2,5-dihydroxypyridine 5,6-dioxygenase (EC 1.13.11.9) | protein | 348 | 29% helix, 28% strand | Q88FY1 |
| E, F | 2,5-dihydroxypyridine 5,6-dioxygenase (EC 1.13.11.9) | protein | 347 | 29% helix, 28% strand | Q88FY1 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 765 | 0.88 | 0.91 | 88 | empty |
| 2 | 771 | 0.87 | 0.90 | 84 | empty |
| 3 | 733 | 0.78 | 0.82 | 99 | empty |
| 4 | 627 | 0.77 | 0.83 | 72 | empty |
| 5 | 427 | 0.76 | 0.85 | 51 | empty |
Interfaces
12 interfaces between chains.
- B–E · 1201 Ų buried · 19 hydrogen bonds · protein-protein
- A–F · 1184 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1181 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1179 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1174 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 7CUP · Structure of 2,5-dihydroxypridine Dioxygenase from Pseudomonas putida KT2440 · 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 E 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 7CUP · PDBe 7CUP · UniProt Q88FY1
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