Research workbench
Dihydroorotate dehydrogenase a from lactococcus lactis complexed with orotate
Analyse Dihydroorotate dehydrogenase a from lactococcus lactis complexed with orotate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DOR
- Type
- protein
- Length
- 622 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotate dehydrogenase a
- EC
- 1.3.3.1
- UniProt
- P54321
- Ligands
- FMN, ORO
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydroorotate dehydrogenase a (EC 1.3.3.1) | protein | 311 | 37% helix, 20% strand | P54321 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- ORO · Orotic acid · ligand · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 305 | 0.77 | 0.89 | 54 | FMN, ORO |
| 2 | 287 | 0.77 | 0.89 | 51 | FMN, ORO |
| 3 | 103 | 0.57 | 0.84 | 12 | empty |
| 4 | 90 | 0.56 | 0.85 | 17 | empty |
| 5 | 85 | 0.56 | 0.86 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2290 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 2DOR · Dihydroorotate dehydrogenase a from lactococcus lactis complexed with orotate · 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 P54321
- Elsewhere: RCSB PDB 2DOR · PDBe 2DOR · UniProt P54321
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