MolNFT v1 · #105939 · protein
Crystal structure of human dihydroorotate dehydrogenase (dhodh) with DH03A347
4RKA · Dihydroorotate dehydrogenase (quinone), mitochondrial: “Crystal structure of human dihydroorotate dehydrogenase (dhodh) with DH03A347”. X-ray diffraction, 4 ligands (FMN, ORO, 3RY), 5 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 4RKA
- Type
- protein
- Length
- 365 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, 3RY, SO4
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 365 | 48% helix, 16% strand | Q02127 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A
- ORO · Orotic acid · ligand · chains A
- 3RY · 2-{[5-(naphthalen-1-ylmethyl)-4-oxo-4H-1lambda~4~,3-thiazol-2-yl]amino}benzoic acid · ligand · chains A
- SO4 · Sulfate ion · ion · 6 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.83 | 0.91 | 64 | FMN, ORO, 3RY |
| 2 | 87 | 0.57 | 0.87 | 18 | empty |
| 3 | 109 | 0.46 | 0.79 | 19 | empty |
| 4 | 92 | 0.44 | 0.80 | 21 | empty |
| 5 | 64 | 0.31 | 0.75 | 16 | empty |
Compared structures
- 4RKA · Crystal structure of human dihydroorotate dehydrogenase (DHODH) with DH03A347 · 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 4RKA · PDBe 4RKA · UniProt Q02127
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