Research workbench
Crystal structure of leishmania major dihydroorotate dehydrogenase mutant D171A
Analyse Crystal structure of leishmania major dihydroorotate dehydrogenase mutant D171A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TRO
- Type
- protein
- Length
- 614 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotate dehydrogenase
- EC
- 1.3.3.1
- UniProt
- Q4QEW7
- Ligands
- FMN, SO4
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydroorotate dehydrogenase (EC 1.3.3.1) | protein | 307 | 40% helix, 23% strand | Q4QEW7 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 8 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 | 602 | 0.76 | 0.82 | 70 | GOL, FMN |
| 2 | 587 | 0.75 | 0.82 | 64 | FMN, GOL |
| 3 | 99 | 0.55 | 0.84 | 14 | empty |
| 4 | 160 | 0.49 | 0.77 | 21 | GOL |
| 5 | 146 | 0.47 | 0.77 | 21 | GOL |
Interfaces
1 interface between chains.
- A–B · 2345 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3TRO · Crystal Structure of Leishmania major dihydroorotate dehydrogenase mutant D171A · 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 Q4QEW7
- Elsewhere: RCSB PDB 3TRO · PDBe 3TRO · UniProt Q4QEW7
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