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Crystal structure of dihydroorotate dehydrogenase from plasmodium falciparum in complex with orotate, FMN, and inhibitor NCGC00600348- 01
Analyse Crystal structure of dihydroorotate dehydrogenase from plasmodium falciparum in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S87
- Type
- protein
- Length
- 752 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
- 8IE, FMN, ORO, P4K, SO4
- Pockets
- 4 · best druggability 0.91
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 379 | 44% helix, 16% strand | Q08210 |
| B | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 373 | 42% helix, 17% strand | Q08210 |
Ligands and binding sites
- 8IE · (4R)-3-methyl-5-[(4R)-4-methyl-3,4-dihydroisoquinolin-2(1H)-yl]thieno[2,3-e][1,2,4]triazolo[4,3-c]pyrimidine · ligand · 4 copies · chains A, B
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- ORO · Orotic acid · ligand · 2 copies · chains A, B
- P4K · polyethylene glycol · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1180 | 0.91 | 0.92 | 129 | 8IE, FMN, ORO |
| 2 | 104 | 0.38 | 0.75 | 24 | empty |
| 3 | 80 | 0.36 | 0.77 | 17 | empty |
| 4 | 67 | 0.34 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 804 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7S87 · Crystal Structure of Dihydroorotate dehydrogenase from Plasmodium falciparum in complex… · 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 7S87 · PDBe 7S87 · UniProt Q08210
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