Research workbench
Crystal structure of hydroxyquinol 1,2-dioxygenase from nocardioides simplex 3E
Analyse Crystal structure of hydroxyquinol 1,2-dioxygenase from nocardioides simplex 3E in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TMX
- Type
- protein
- Length
- 579 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydroxyquinol 1,2-dioxygenase
- EC
- 1.13.11.37
- UniProt
- Q5PXQ6
- Ligands
- HGX, BEZ, FE, CU, SO4, CL
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydroxyquinol 1,2-dioxygenase (EC 1.13.11.37) | protein | 292 | 32% helix, 22% strand | Q5PXQ6 |
| B | Hydroxyquinol 1,2-dioxygenase (EC 1.13.11.37) | protein | 287 | 31% helix, 21% strand | — |
Ligands and binding sites
- HGX · 1-heptadecanoyl-2-tridecanoyl-3-glycerol-phosphonyl choline · ligand · 2 copies · chains A, B
- BEZ · Benzoic acid · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- CU · Copper (II) ion · metal · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 940 | 0.86 | 0.87 | 55 | HGX |
| 2 | 269 | 0.61 | 0.79 | 41 | BEZ |
| 3 | 213 | 0.57 | 0.79 | 31 | empty |
| 4 | 61 | 0.46 | 0.84 | 14 | empty |
| 5 | 57 | 0.36 | 0.79 | 15 | SO4 |
Interfaces
1 interface between chains.
- A–B · 3284 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 1TMX · Crystal structure of hydroxyquinol 1,2-dioxygenase from Nocardioides Simplex 3E · the same entry in another collection · chain A against A, TM-score 1.00
- Q5PXQ6 · AlphaFold monomer V2.0 prediction for hydroxyquinol 1,2-dioxygenase (Q5PXQ6) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q5PXQ6
- Elsewhere: RCSB PDB 1TMX · PDBe 1TMX · UniProt Q5PXQ6
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