Research workbench
Crystal structure of human dihydroorotate dehydrogenase (dhodh) with DH03A016
Analyse Crystal structure of human dihydroorotate dehydrogenase (dhodh) with DH03A016 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JGD
- Type
- protein
- Length
- 364 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, DET, 4JG, SO4
- Pockets
- 5 · best druggability 0.83
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 | 364 | 46% helix, 16% strand | Q02127 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A
- ORO · Orotic acid · ligand · chains A
- DET · Undecylamine-N,N-dimethyl-N-oxide · ligand · chains A
- 4JG · 1-[4-methyl-2-(naphthalen-2-ylamino)-1,3-thiazol-5-yl]ethanone · ligand · chains A
- SO4 · Sulfate ion · ion · 9 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 431 | 0.83 | 0.91 | 62 | FMN, ORO, 4JG |
| 2 | 94 | 0.44 | 0.80 | 19 | DET |
| 3 | 51 | 0.41 | 0.82 | 17 | SO4 |
| 4 | 89 | 0.40 | 0.78 | 20 | empty |
| 5 | 79 | 0.36 | 0.76 | 19 | empty |
Compared structures
- 4JGD · Crystal structure of human dihydroorotate dehydrogenase (DHODH) with DH03A016 · 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 4JGD · PDBe 4JGD · UniProt Q02127
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