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Quaternary complex of human dihydroorotate dehydrogenase (dhodh) with flavin mononucleotide (FMN), orotic acid and ag-636
Analyse Quaternary complex of human dihydroorotate dehydrogenase (dhodh) with flavin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VND
- Type
- protein
- Length
- 365 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotate dehydrogenase (quinone), mitochondrial
- EC
- 1.3.5.2
- UniProt
- Q02127
- Ligands
- DET, DDQ, R4P, FMN, ORO, NA, CL
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 365 | 46% helix, 16% strand | Q02127 |
Ligands and binding sites
- DET · Undecylamine-N,N-dimethyl-N-oxide · ligand · 2 copies · chains A
- DDQ · Decylamine-N,N-dimethyl-N-oxide · ligand · 2 copies · chains A
- R4P · 1-methyl-5-(2'-methyl[1,1'-biphenyl]-4-yl)-1H-benzotriazole-7-carboxylic acid · ligand · chains A
- FMN · Flavin mononucleotide · ligand · chains A
- ORO · Orotic acid · ligand · chains A
- NA · Sodium ion · metal · 3 copies · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 6 copies · chains A
- ACT · Acetate ion · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.84 | 0.91 | 63 | R4P, DDQ, FMN, ORO |
| 2 | 110 | 0.53 | 0.83 | 25 | empty |
| 3 | 77 | 0.47 | 0.83 | 18 | DET, NA |
| 4 | 89 | 0.40 | 0.78 | 21 | GOL |
Compared structures
- 6VND · Quaternary Complex of human dihydroorotate dehydrogenase (DHODH) with flavin… · 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 Q02127
- Elsewhere: RCSB PDB 6VND · PDBe 6VND · UniProt Q02127
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