Research workbench
Crystal structure of dihydroorotate dehydrogenase from leishmania major in complex with 5-nitroorotic acid
Analyse Crystal structure of dihydroorotate dehydrogenase from leishmania major in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MHU
- Type
- protein
- Length
- 615 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, EJZ, SO4
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase (EC 1.3.3.1) | protein | 307 | 40% helix, 24% strand | Q4QEW7 |
| B | Dihydroorotate dehydrogenase (EC 1.3.3.1) | protein | 308 | 39% helix, 23% strand | Q4QEW7 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- EJZ · 5-nitro-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 5 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 | 409 | 0.78 | 0.87 | 69 | GOL, FMN, EJZ |
| 2 | 487 | 0.77 | 0.85 | 68 | FMN, EJZ, GOL |
| 3 | 83 | 0.60 | 0.88 | 15 | empty |
| 4 | 152 | 0.48 | 0.77 | 20 | GOL |
| 5 | 123 | 0.45 | 0.77 | 19 | GOL |
Interfaces
1 interface between chains.
- A–B · 2228 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3MHU · Crystal structure of dihydroorotate dehydrogenase from Leishmania major in complex with… · the same entry in another collection · chain B against B, 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 3MHU · PDBe 3MHU · UniProt Q4QEW7
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