MolNFT v1 · #139443 · protein
Crystal structures of FMN-free form of dihydroorotate dehydrogenase from trypanosoma brucei
5XFW · Dihydroorotate dehydrogenase (fumarate): “Crystal structures of FMN-free form of dihydroorotate dehydrogenase from trypanosoma brucei”. X-ray diffraction, 14 pockets (best druggability 0.81). MolNFT v1 #139443 on GenesisL1: 3D…
- PDB
- 5XFW
- Type
- protein
- Length
- 1,253 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
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydroorotate dehydrogenase (fumarate) (EC 1.3.98.1) | protein | 313 | 39% helix, 23% strand | Q57U83 |
| C | Dihydroorotate dehydrogenase (fumarate) (EC 1.3.98.1) | protein | 312 | 40% helix, 23% strand | Q57U83 |
| D | Dihydroorotate dehydrogenase (fumarate) (EC 1.3.98.1) | protein | 315 | 39% helix, 23% strand | Q57U83 |
Ligands and binding sites
- MLI · Malonate ion · additive · 15 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 500 | 0.81 | 0.88 | 66 | MLI |
| 2 | 166 | 0.80 | 0.96 | 39 | MLI |
| 3 | 556 | 0.80 | 0.86 | 75 | MLI |
| 4 | 265 | 0.77 | 0.89 | 48 | MLI |
| 5 | 248 | 0.68 | 0.84 | 53 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2449 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 2407 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 632 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 30 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 25 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5XFW · Crystal structures of FMN-free 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 C 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 5XFW · PDBe 5XFW · UniProt Q57U83
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