Research workbench
Crystal structure of leishmania major dihydroorotate dehydrogenase mutant Y142A
Analyse Crystal structure of leishmania major dihydroorotate dehydrogenase mutant Y142A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DGS
- Type
- protein
- Length
- 606 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
- Q4QEW7
- Ligands
- FMN, SO4
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydroorotate dehydrogenase (fumarate) (EC 1.3.98.1) | protein | 303 | 40% helix, 24% strand | Q4QEW7 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.80 | 0.81 | 126 | FMN |
| 2 | 128 | 0.46 | 0.77 | 21 | GOL, SO4 |
| 3 | 114 | 0.45 | 0.78 | 20 | GOL, SO4 |
Interfaces
1 interface between chains.
- A–B · 2202 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 6DGS · Crystal Structure of Leishmania major dihydroorotate dehydrogenase mutant Y142A · 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 6DGS · PDBe 6DGS · UniProt Q4QEW7
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