Research workbench
Structure of human dihydroorotate dehydrogenase in complex with mii-4- 097
Analyse Structure of human dihydroorotate dehydrogenase in complex with mii-4- 097 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3W7R
- Type
- protein
- Length
- 367 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotate dehydrogenase (quinone), mitochondrial
- EC
- 1.3.5.2
- UniProt
- Q02127
- Ligands
- DDQ, W7A, FMN, ORO, SO4, CL
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 367 | 47% helix, 16% strand | Q02127 |
Ligands and binding sites
- DDQ · Decylamine-N,N-dimethyl-N-oxide · ligand · 6 copies · chains A
- W7A · 2,6-dioxo-5-[2-(4-phenylphenyl)ethyl]-1,2,3,6- tetrahydropyrimidine-4-carboxylic acid · ligand · chains A
- FMN · Flavin mononucleotide · ligand · chains A
- ORO · Orotic acid · ligand · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 22 copies · chains A
- ACT · Acetate ion · additive · 7 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.83 | 0.91 | 57 | W7A, FMN, ORO |
| 2 | 86 | 0.51 | 0.84 | 27 | GOL |
| 3 | 84 | 0.43 | 0.80 | 20 | GOL |
| 4 | 69 | 0.38 | 0.79 | 19 | GOL, ACT |
Compared structures
- 3W7R · Structure of Human dihydroorotate dehydrogenase in complex with mii-4-097 · the same entry in another collection · chain A against A, TM-score 1.00
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 Q02127
- Elsewhere: RCSB PDB 3W7R · PDBe 3W7R · UniProt Q02127
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