MolNFT v1 · #117510 · protein
Crystal structure of trypanosoma cruzi dihydroorotate dehydrogenase in complex with NEQ0130
5EA9 · Dihydroorotate dehydrogenase (fumarate): “Crystal structure of trypanosoma cruzi dihydroorotate dehydrogenase in complex with NEQ0130”. X-ray diffraction, 3 ligands (5LM, FMN, NCO), 7 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 5EA9
- 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
- 5LM, FMN, NCO
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydroorotate dehydrogenase (fumarate) (EC 1.3.98.1) | protein | 313 | 40% helix, 21% strand | Q4D3W2 |
Ligands and binding sites
- 5LM · 5-[(E)-3-thiophen-2-ylprop-2-enylidene]-1,3-diazinane-2,4,6-trione · ligand · 2 copies · chains A, B
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- NCO · Cobalt hexammine(iii) · ligand · 2 copies · chains B
- GOL · Glycerol · additive · 13 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, 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 | 363 | 0.80 | 0.90 | 60 | 5LM, GOL, FMN |
| 2 | 341 | 0.79 | 0.89 | 63 | 5LM, GOL, FMN |
| 3 | 105 | 0.55 | 0.83 | 21 | GOL |
| 4 | 118 | 0.46 | 0.78 | 19 | GOL |
| 5 | 121 | 0.45 | 0.77 | 19 | EDO |
Interfaces
1 interface between chains.
- A–B · 2286 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5EA9 · 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 5EA9 · PDBe 5EA9 · UniProt Q4D3W2
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