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Structure of human dihydroorotate dehydrogenase in complex with 275-10-COOMe
Analyse Structure of human dihydroorotate dehydrogenase in complex with 275-10-COOMe in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZF4
- Type
- protein
- Length
- 366 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.66
- Source
- Homo sapiens
- Molecule
- Dihydroorotate dehydrogenase (quinone), mitochondrial
- EC
- 1.3.5.2
- UniProt
- Q02127
- Ligands
- FMN, ORO, 9BL, SO4
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · resolution 1.66 · 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 | 366 | 47% helix, 16% strand | Q02127 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A
- ORO · Orotic acid · ligand · chains A
- 9BL · methyl (2E,6E)-8-(3-chloro-5-formyl-2,6-dihydroxy-4-methylphenyl)-2,6-dimethylocta-2,6-dienoate · ligand · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- ACT · Acetate ion · additive · 5 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 | 393 | 0.85 | 0.93 | 65 | FMN, ORO, 9BL |
| 2 | 66 | 0.55 | 0.87 | 19 | empty |
| 3 | 96 | 0.43 | 0.79 | 18 | SO4, ACT |
| 4 | 96 | 0.42 | 0.78 | 22 | ACT |
Compared structures
- 5ZF4 · Structure of human dihydroorotate dehydrogenase in complex with 275- 10-coome · the same entry in another collection · chain A against A, TM-score 1.00
- Q02127 · AlphaFold monomer V2.0 prediction for dihydroorotate dehydrogenase (quinone)… · a predicted model of the same protein · chain A 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 Q02127
- Elsewhere: RCSB PDB 5ZF4 · PDBe 5ZF4 · UniProt Q02127
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