Research workbench
Crystal structure of trypanosoma cruzi dihydroorotate dehydrogenase in complex with oxonate
Analyse Crystal structure of trypanosoma cruzi dihydroorotate dehydrogenase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2E6F
- Type
- protein
- Length
- 624 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotate dehydrogenase
- EC
- 1.3.3.1
- UniProt
- Q4D3W2
- Ligands
- FMN, OXC, NCO
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydroorotate dehydrogenase (EC 1.3.3.1) | protein | 312 | 39% helix, 21% strand | Q4D3W2 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- OXC · Oxonic acid · ligand · 2 copies · chains A, B
- NCO · Cobalt hexammine(iii) · ligand · chains A
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.78 | 0.90 | 48 | FMN, OXC |
| 2 | 249 | 0.77 | 0.90 | 42 | FMN, OXC |
| 3 | 77 | 0.56 | 0.86 | 16 | empty |
| 4 | 64 | 0.46 | 0.84 | 21 | empty |
| 5 | 54 | 0.44 | 0.84 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2231 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 2E6F · Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with… · 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 2E6F · PDBe 2E6F · UniProt Q4D3W2
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