MolNFT v1 · #117468 · protein
Crystal structure of trypanosoma cruzi dihydroorotate dehydrogenase in complex with NEQ0071
5E93 · Dihydroorotate dehydrogenase (fumarate): “Crystal structure of trypanosoma cruzi dihydroorotate dehydrogenase in complex with NEQ0071”. X-ray diffraction, 3 ligands (NCO, 5LL, FMN), 7 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 5E93
- Type
- protein
- Length
- 626 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotate dehydrogenase (fumarate)
- EC
- 1.3.98.1
- UniProt
- Q4D3W2
- Ligands
- NCO, 5LL, FMN
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydroorotate dehydrogenase (fumarate) (EC 1.3.98.1) | protein | 313 | 40% helix, 22% strand | Q4D3W2 |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 3 copies · chains A, B
- 5LL · 5-[(E)-3-(furan-2-yl)prop-2-enylidene]-1,3-diazinane-2,4,6-trione · ligand · 2 copies · chains A, B
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 23 copies · chains A, B
- GOL · Glycerol · additive · 12 copies · chains A, B
- CAC · Cacodylate ion · additive · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 354 | 0.80 | 0.90 | 63 | 5LL, GOL, FMN, CAC |
| 2 | 360 | 0.79 | 0.89 | 66 | 5LL, GOL, FMN |
| 3 | 78 | 0.54 | 0.85 | 15 | GOL |
| 4 | 126 | 0.44 | 0.76 | 19 | EDO |
| 5 | 114 | 0.44 | 0.77 | 21 | GOL, EDO |
Interfaces
1 interface between chains.
- A–B · 2278 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5E93 · Crystal Structure of Trypanosoma cruzi Dihydroorotate Dehydrogenase in Complex 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 Q4D3W2
- Elsewhere: RCSB PDB 5E93 · PDBe 5E93 · UniProt Q4D3W2
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