MolNFT v1 · #150093 · protein
Plasmodium falciparum dihydroorotate dehydrogenase dhodh in complex with 3,6-dimethyl-N-(4-(TRIFLUOROMETHYL)PHENYL)-(1,2)OXAZOLO(5,4-D) pyrimidin-4-amine
6GJG · Dihydroorotate dehydrogenase (quinone), mitochondrial: “Plasmodium falciparum dihydroorotate dehydrogenase dhodh in complex with…”. X-ray diffraction, 3 ligands (FMN, ORO, F1T), 6 pockets (best druggability 0.84). MolNFT v1 #150093…
- PDB
- 6GJG
- Type
- protein
- Length
- 744 residues
- Chains
- 2
- 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
- FMN, ORO, F1T
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 371 | 44% helix, 16% strand | Q08210 |
| B | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 373 | 45% helix, 16% strand | Q08210 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- ORO · Orotic acid · ligand · 2 copies · chains A, B
- F1T · 3,6-dimethyl-~{N}-[4-(trifluoromethyl)phenyl]-[1, 2]oxazolo[5,4-d]pyrimidin-4-amine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 372 | 0.84 | 0.93 | 70 | FMN, ORO, F1T |
| 2 | 822 | 0.83 | 0.85 | 93 | FMN, ORO, F1T |
| 3 | 308 | 0.55 | 0.75 | 23 | empty |
| 4 | 125 | 0.44 | 0.77 | 21 | empty |
| 5 | 91 | 0.42 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 513 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6GJG · Plasmodium falciparum dihydroorotate dehydrogenase DHODH in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q08210 · AlphaFold monomer V2.0 prediction for dihydroorotate dehydrogenase (quinone)… · a predicted model of the same protein · chain B 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 6GJG · PDBe 6GJG · UniProt Q08210
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