Research workbench
Crystal structure of dhodh in complex with ferulenol from eimeria tenella
Analyse Crystal structure of dhodh in complex with ferulenol from eimeria tenella in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AJE
- Type
- protein
- Length
- 1,506 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotate dehydrogenase (quinone), mitochondrial
- EC
- 1.3.5.2
- UniProt
- U6KL66
- Ligands
- FMN, ORO, 9AU
- Pockets
- 17 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 378 | 35% helix, 16% strand | U6KL66 |
| B, C, D | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 376 | 37% helix, 16% strand | U6KL66 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- ORO · Orotic acid · ligand · 4 copies · chains A, B, C, D
- 9AU · 4-oxidanyl-3-[(2~{E},6~{E})-3,7,11-trimethyldodeca-2,6, 10-trienyl]chromen-2-one · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1179 | 0.86 | 0.86 | 146 | FMN, ORO, 9AU |
| 2 | 485 | 0.79 | 0.86 | 66 | FMN, ORO, 9AU |
| 3 | 455 | 0.78 | 0.86 | 70 | FMN, ORO, 9AU |
| 4 | 270 | 0.78 | 0.91 | 49 | FMN, ORO |
| 5 | 51 | 0.68 | 0.97 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–C · 753 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 719 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 619 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 25 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6AJE · Crystal structure of DHODH in complex with ferulenol from Eimeria tenella · 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 U6KL66
- Elsewhere: RCSB PDB 6AJE · PDBe 6AJE · UniProt U6KL66
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