Research workbench
Crystal structure of leishmania major dihydroorotate dehydrogenase mutant Q139A
Analyse Crystal structure of leishmania major dihydroorotate dehydrogenase mutant Q139A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DWG
- Type
- protein
- Length
- 613 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, NI, SO4
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase (fumarate) (EC 1.3.98.1) | protein | 306 | 41% helix, 23% strand | Q4QEW7 |
| B | Dihydroorotate dehydrogenase (fumarate) (EC 1.3.98.1) | protein | 307 | 40% helix, 23% strand | Q4QEW7 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 601 | 0.76 | 0.83 | 70 | FMN, GOL |
| 2 | 576 | 0.74 | 0.82 | 68 | FMN |
| 3 | 118 | 0.61 | 0.86 | 16 | NI |
| 4 | 140 | 0.48 | 0.77 | 21 | GOL |
| 5 | 144 | 0.47 | 0.77 | 19 | SO4, GOL |
Interfaces
1 interface between chains.
- A–B · 2324 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6DWG · Crystal structure of Leishmania major dihydroorotate dehydrogenase mutant Q139A · 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 6DWG · PDBe 6DWG · UniProt Q4QEW7
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