Research workbench
Structure of human dihydroorotate dehydrogenase in complex with 287- 12-ocoipr
Analyse Structure of human dihydroorotate dehydrogenase in complex with 287- 12-ocoipr in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZFA
- Type
- protein
- Length
- 366 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
- FMN, ORO, 9BU, SO4
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 366 | 46% helix, 16% strand | Q02127 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A
- ORO · Orotic acid · ligand · chains A
- 9BU · (2E,6E)-8-(3-chloro-5-formyl-2,6-dihydroxy-4-methylphenyl)-3,6-dimethylocta-2,6-dien-1-yl 2-methylpropanoate · ligand · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- ACT · Acetate ion · additive · 3 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 | 488 | 0.84 | 0.90 | 66 | FMN, ORO, 9BU |
| 2 | 51 | 0.54 | 0.89 | 18 | empty |
| 3 | 107 | 0.45 | 0.79 | 23 | empty |
| 4 | 70 | 0.42 | 0.81 | 14 | ACT |
Compared structures
- 5ZFA · Structure of human dihydroorotate dehydrogenase in complex with 287-12-OCOiPr · 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 5ZFA · PDBe 5ZFA · UniProt Q02127
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