MolNFT v1 · #83120 · protein
Structure of trypanosoma cruzi dihydroorotate dehydrogenase in complex with sh-1-103
3W87 · Dihydroorotate dehydrogenase (fumarate): “Structure of trypanosoma cruzi dihydroorotate dehydrogenase in complex with sh-1-103”. X-ray diffraction, 3 ligands (W87, FMN, NCO), 6 pockets (best druggability 0.81). MolNFT v1 #83120 on…
- PDB
- 3W87
- Type
- protein
- Length
- 628 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
- W87, FMN, NCO
- Pockets
- 6 · best druggability 0.81
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 | 314 | 39% helix, 22% strand | Q4D3W2 |
Ligands and binding sites
- W87 · 5-{4-[5-(methoxycarbonyl)naphthalen-2-yl]butyl}-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 · 2 copies · chains A
- GOL · Glycerol · additive · 25 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 24 copies · chains A, B
- CAC · Cacodylate ion · additive · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 562 | 0.81 | 0.87 | 61 | W87, GOL, FMN |
| 2 | 635 | 0.78 | 0.84 | 63 | W87, GOL, CAC, FMN |
| 3 | 149 | 0.54 | 0.80 | 26 | PEG |
| 4 | 123 | 0.46 | 0.77 | 19 | GOL |
| 5 | 121 | 0.44 | 0.77 | 19 | GOL |
Interfaces
1 interface between chains.
- A–B · 2457 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 3W87 · Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with SH-1-103 · 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 3W87 · PDBe 3W87 · UniProt Q4D3W2
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