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Crystal structure of 4-chlorocatechol dioxygenase from rhodococcus opacus 1CP in complex with hydroxyquinol
Analyse Crystal structure of 4-chlorocatechol dioxygenase from rhodococcus opacus 1CP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O6J
- Type
- protein
- Length
- 512 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chlorocatechol 1,2-dioxygenase
- EC
- 1.13.11.-
- UniProt
- O67987
- Ligands
- MYY, HQN, FE, CL
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Chlorocatechol 1,2-dioxygenase (EC 1.13.11.-) | protein | 256 | 25% helix, 25% strand | O67987 |
Ligands and binding sites
- MYY · (2R)-3-(phosphonooxy)-2-(tetradecanoyloxy)propyl palmitate · ligand · 2 copies · chains A, B
- HQN · benzene-1,2,4-triol · ligand · chains A
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 792 | 0.86 | 0.88 | 49 | MYY |
| 2 | 118 | 0.55 | 0.83 | 24 | empty |
| 3 | 157 | 0.50 | 0.78 | 25 | empty |
| 4 | 137 | 0.44 | 0.77 | 25 | empty |
| 5 | 55 | 0.36 | 0.79 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2461 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 3O6J · Crystal Structure of 4-Chlorocatechol Dioxygenase from Rhodococcus opacus 1CP in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- O67987 · AlphaFold monomer V2.0 prediction for chlorocatechol 1,2-dioxygenase (O67987) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O67987
- Elsewhere: RCSB PDB 3O6J · PDBe 3O6J · UniProt O67987
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