Research workbench
Rat dihydroorotate dehydrogenase (DHOD)in complex with atovaquone
Analyse Rat dihydroorotate dehydrogenase (DHOD)in complex with atovaquone in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UUM
- Type
- protein
- Length
- 700 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- RATTUS RATTUS
- Molecule
- Dihydroorotate dehydrogenase
- EC
- 1.3.99.11
- UniProt
- Q63707
- Ligands
- FMN, ORO, AFI
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.3 · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydroorotate dehydrogenase (EC 1.3.99.11) | protein | 350 | 45% helix, 17% strand | Q63707 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- ORO · Orotic acid · ligand · 2 copies · chains A, B
- AFI · 2-[4-(4-chlorophenyl)cyclohexylidene]-3,4-dihydroxy-1(2H)-naphthalenone · ligand · 2 copies · chains A, B
- BOG · octyl beta-D-glucopyranoside · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.82 | 0.88 | 75 | FMN, ORO, AFI |
| 2 | 543 | 0.81 | 0.87 | 81 | FMN, ORO, AFI |
| 3 | 77 | 0.50 | 0.84 | 16 | empty |
| 4 | 77 | 0.49 | 0.84 | 17 | empty |
| 5 | 155 | 0.44 | 0.75 | 27 | empty |
Compared structures
- 1UUM · Rat dihydroorotate dehydrogenase (DHOD)IN complex with atovaquone · the same entry in another collection · chain A against A, TM-score 1.00
- Q63707 · AlphaFold monomer V2.0 prediction for dihydroorotate dehydrogenase (quinone)… · 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 Q63707
- Elsewhere: RCSB PDB 1UUM · PDBe 1UUM · UniProt Q63707
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