Research workbench
Crystal structure of plasmodium falciparum dihydroorotate dehydrogenase bound with inhibitor DSM589 (ethyl 3-methyl-4-((4- (TRIFLUOROMETHYL)BENZO[D]OXAZOL-7-YL)METHYL)-1H-pyrrole-2- carboxylate)
Analyse Crystal structure of plasmodium falciparum dihydroorotate dehydrogenase bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KYK
- Type
- protein
- Length
- 1,484 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotate dehydrogenase (quinone), mitochondrial
- EC
- 1.3.5.2
- UniProt
- Q08210
- Ligands
- XAJ, FMN, ORO
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 376 | 44% helix, 17% strand | Q08210 |
| B | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 370 | 42% helix, 17% strand | Q08210 |
| C | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 369 | 44% helix, 16% strand | Q08210 |
| D | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 369 | 45% helix, 17% strand | Q08210 |
Ligands and binding sites
- XAJ · ethyl 3-methyl-4-{[4-(trifluoromethyl)-1,3-benzoxazol-7-yl]methyl}-1H-pyrrole-2-carboxylate · ligand · 4 copies · chains A, B, C, D
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- ORO · Orotic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 358 | 0.85 | 0.94 | 55 | XAJ, FMN, ORO |
| 2 | 370 | 0.84 | 0.93 | 52 | XAJ, FMN, ORO |
| 3 | 1136 | 0.83 | 0.84 | 82 | empty |
| 4 | 442 | 0.82 | 0.90 | 63 | XAJ, FMN, ORO |
| 5 | 807 | 0.82 | 0.85 | 92 | XAJ, FMN, ORO |
Interfaces
3 interfaces between chains.
- A–B · 481 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 287 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 189 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7KYK · Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with… · the same entry in another collection · chain D against D, TM-score 1.00
- Q08210 · AlphaFold monomer V2.0 prediction for dihydroorotate dehydrogenase (quinone)… · a predicted model of the same protein · chain C 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 Q08210
- Elsewhere: RCSB PDB 7KYK · PDBe 7KYK · UniProt Q08210
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