Research workbench
Plasmodium falciparum dihydroorotate dehydrogenase (dhodh) co- crystallized with N-(2,2-diphenylethyl)-4-hydroxy-1,2,5-thiadiazole- 3-carboxamide
Analyse Plasmodium falciparum dihydroorotate dehydrogenase (dhodh) co- crystallized… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I55
- Type
- protein
- Length
- 747 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotate dehydrogenase
- UniProt
- Q54A96
- Ligands
- FMN, ORO, DZB
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase | protein | 379 | 45% helix, 16% strand | Q54A96 |
| B | Dihydroorotate dehydrogenase | protein | 368 | 44% helix, 17% strand | Q54A96 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- ORO · Orotic acid · ligand · 2 copies · chains A, B
- DZB · N-(2,2-Diphenylethyl)-4-hydroxy-1,2,5-thiadiazole-3-carboxamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.83 | 0.89 | 73 | DZB, FMN, ORO |
| 2 | 861 | 0.82 | 0.84 | 97 | FMN, ORO, DZB |
| 3 | 308 | 0.54 | 0.75 | 22 | empty |
| 4 | 105 | 0.42 | 0.78 | 21 | empty |
| 5 | 113 | 0.39 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 463 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6I55 · Plasmodium falciparum dihydroorotate dehydrogenase (DHODH) co-crystallized with… · 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 Q54A96
- Elsewhere: RCSB PDB 6I55 · PDBe 6I55 · UniProt Q54A96
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