Research workbench
Crystal structure of leishmania major dihydroorotate dehydrogenase mutant H174A in complex with orotate
Analyse Crystal structure of leishmania major dihydroorotate dehydrogenase mutant H174A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EBS
- Type
- protein
- Length
- 626 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, ORO, NI, SO4
- Pockets
- 8 · best druggability 0.79
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 | 313 | 40% helix, 24% strand | Q4QEW7 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- ORO · Orotic acid · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · chains B
- SO4 · Sulfate ion · ion · 6 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
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.79 | 0.92 | 43 | FMN, ORO |
| 2 | 250 | 0.79 | 0.92 | 43 | FMN, ORO |
| 3 | 206 | 0.57 | 0.79 | 25 | NI |
| 4 | 164 | 0.49 | 0.77 | 21 | GOL, SO4 |
| 5 | 99 | 0.48 | 0.81 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2233 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6EBS · Crystal structure of Leishmania major dihydroorotate dehydrogenase mutant H174A in… · 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 6EBS · PDBe 6EBS · UniProt Q4QEW7
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