Research workbench
Crystal structure of dihydroorotate dehydrogenase from trypanosoma cruzi strain Y
Analyse Crystal structure of dihydroorotate dehydrogenase from trypanosoma cruzi strain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C3N
- Type
- protein
- Length
- 1,244 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotate dehydrogenase
- UniProt
- Q4D3W2
- Ligands
- FMN, SO4
- Pockets
- 11 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Dihydroorotate dehydrogenase | protein | 311 | 40% helix, 22% strand | Q4D3W2 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 785 | 0.87 | 0.90 | 86 | empty |
| 2 | 185 | 0.79 | 0.94 | 38 | FMN, SO4 |
| 3 | 221 | 0.77 | 0.91 | 45 | FMN, SO4 |
| 4 | 370 | 0.77 | 0.87 | 64 | FMN, SO4, GOL |
| 5 | 216 | 0.76 | 0.91 | 44 | FMN, SO4 |
Interfaces
6 interfaces between chains.
- A–D · 2205 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 2201 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 665 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 641 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 102 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3C3N · Crystal structure of dihydroorotate dehydrogenase from Trypanosoma cruzi strain Y · the same entry in another collection · chain A against A, TM-score 1.00
- Q4D3W2 · AlphaFold monomer V2.0 prediction for dihydroorotate dehydrogenase (fumarate) (Q4D3W2) · a predicted model of the same protein · 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 3C3N · PDBe 3C3N · UniProt Q4D3W2
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