Research workbench
Structure of trypanosoma cruzi dihydroorotate dehydrogenase in complex with mii-4-065
Analyse Structure of trypanosoma cruzi dihydroorotate dehydrogenase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JD4
- 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
- JDM, FMN, NCO
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydroorotate dehydrogenase (fumarate) (EC 1.3.98.1) | protein | 313 | 39% helix, 22% strand | Q4D3W2 |
Ligands and binding sites
- JDM · 5-{2-[2-(hydroxymethyl)phenyl]ethyl}-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid · ligand · 2 copies · chains A, B
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- NCO · Cobalt hexammine(iii) · ligand · chains B
- GOL · Glycerol · additive · 18 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 | 666 | 0.78 | 0.83 | 66 | JDM, GOL, FMN |
| 2 | 629 | 0.78 | 0.83 | 62 | JDM, GOL, FMN |
| 3 | 153 | 0.55 | 0.81 | 24 | GOL |
| 4 | 135 | 0.45 | 0.76 | 19 | empty |
| 5 | 122 | 0.45 | 0.77 | 19 | GOL |
Interfaces
1 interface between chains.
- A–B · 2389 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 4JD4 · Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-4-065 · 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 4JD4 · PDBe 4JD4 · UniProt Q4D3W2
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