MolNFT v1 · #90301 · protein
Crystal structure of dihydroorotate dehydrogenase from leishmania major in complex with 4-nitrophenyl isothiocyanate
4EF9: “Crystal structure of dihydroorotate dehydrogenase from leishmania major in complex with 4-nitrophenyl…”. X-ray diffraction, 3 ligands (4NF, FMN, SO4), 7 pockets (best druggability 0.79). MolNFT v1 #90301 on GenesisL1: 3D structure…
- PDB
- 4EF9
- Type
- protein
- Length
- 626 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
- 4NF, FMN, SO4
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydroorotate dehydrogenase (EC 1.3.3.1) | protein | 313 | 40% helix, 22% strand | Q4QEW7 |
Ligands and binding sites
- 4NF · N-(4-nitrophenyl)thioformamide · ligand · 2 copies · chains A, B
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 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
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 248 | 0.79 | 0.92 | 41 | FMN, SO4 |
| 2 | 237 | 0.78 | 0.92 | 45 | FMN, SO4 |
| 3 | 93 | 0.57 | 0.86 | 17 | empty |
| 4 | 95 | 0.57 | 0.86 | 24 | 4NF |
| 5 | 137 | 0.47 | 0.77 | 19 | GOL |
Interfaces
1 interface between chains.
- A–B · 2292 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4EF9 · Crystal structure of dihydroorotate dehydrogenase from Leishmania major in complex with… · 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 4EF9 · PDBe 4EF9 · UniProt Q4QEW7
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