MolNFT v1 · #124242 · protein
Crystal structure of human dihydroorotate dehydrogenase at 1.7 a resolution
5K9D · Dihydroorotate dehydrogenase (quinone), mitochondrial: “Crystal structure of human dihydroorotate dehydrogenase at 1.7 a resolution”. X-ray diffraction, 5 ligands (FNR, ORO, CE9), 3 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 5K9D
- Type
- protein
- Length
- 359 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
- FNR, ORO, CE9, CL, SO4
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 359 | 45% helix, 17% strand | Q02127 |
Ligands and binding sites
- FNR · 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydro-2H-benzo[g]pteridin-1-id-10(5H)-yl)-5-O-phosphonato-D-ribitol · ligand · chains A
- ORO · Orotic acid · ligand · chains A
- CE9 · Dodecyl nona ethylene glycol ether · ligand · chains A
- CL · Chloride ion · ion · 3 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- ACT · Acetate ion · additive · 3 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.82 | 0.90 | 63 | FNR, ORO, CE9 |
| 2 | 79 | 0.41 | 0.79 | 19 | empty |
| 3 | 76 | 0.39 | 0.79 | 18 | ACT |
Compared structures
- 5K9D · Crystal structure of human dihydroorotate dehydrogenase at 1.7 A resolution · 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 5K9D · PDBe 5K9D · UniProt Q02127
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