Research workbench
Crystal structures of FMN-bound form of dihydroorotate dehydrogenase from trypanosoma brucei
Analyse Crystal structures of FMN-bound form of dihydroorotate dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XFV
- Type
- protein
- Length
- 1,248 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotate dehydrogenase (fumarate)
- EC
- 1.3.98.1
- UniProt
- Q57U83
- Ligands
- FMN
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Dihydroorotate dehydrogenase (fumarate) (EC 1.3.98.1) | protein | 312 | 39% helix, 23% strand | Q57U83 |
| B | Dihydroorotate dehydrogenase (fumarate) (EC 1.3.98.1) | protein | 311 | 40% helix, 23% strand | Q57U83 |
| D | Dihydroorotate dehydrogenase (fumarate) (EC 1.3.98.1) | protein | 313 | 39% helix, 23% strand | Q57U83 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- MLI · Malonate ion · additive · 11 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.80 | 0.94 | 38 | FMN, MLI |
| 2 | 475 | 0.80 | 0.88 | 67 | FMN, MLI |
| 3 | 517 | 0.80 | 0.87 | 75 | MLI, FMN |
| 4 | 244 | 0.79 | 0.92 | 43 | FMN, MLI |
| 5 | 351 | 0.60 | 0.77 | 36 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2357 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2325 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 619 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 77 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5XFV · Crystal structures of FMN-bound form of dihydroorotate dehydrogenase from Trypanosoma… · the same entry in another collection · chain A against A, TM-score 1.00
- Q57U83 · AlphaFold monomer V2.0 prediction for dihydroorotate dehydrogenase (fumarate) (Q57U83) · a predicted model of the same protein · chain B 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 Q57U83
- Elsewhere: RCSB PDB 5XFV · PDBe 5XFV · UniProt Q57U83
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