Research workbench
E. COLI dihydroorotate dehydrogenase bound to the ubiquinone surrogate dcip
Analyse E. COLI dihydroorotate dehydrogenase bound to the ubiquinone surrogate dcip in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7T6C
- Type
- protein
- Length
- 670 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotate dehydrogenase (quinone)
- EC
- 1.3.5.2
- UniProt
- P0A7E1
- Ligands
- ORO, RLM, FMN
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydroorotate dehydrogenase (quinone) (EC 1.3.5.2) | protein | 335 | 41% helix, 18% strand | P0A7E1 |
Ligands and binding sites
- ORO · Orotic acid · ligand · 2 copies · chains A, B
- RLM · 2,6-bis(chloranyl)-4-[(4-hydroxyphenyl)amino]phenol · ligand · 2 copies · chains A, B
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains A
- GOL · Glycerol · additive · chains 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 | 576 | 0.82 | 0.87 | 72 | ORO, RLM, FMN |
| 2 | 540 | 0.81 | 0.87 | 79 | ORO, RLM, FMN |
| 3 | 559 | 0.70 | 0.79 | 41 | empty |
| 4 | 78 | 0.35 | 0.76 | 16 | empty |
| 5 | 56 | 0.28 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 993 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 7T6C · E. coli dihydroorotate dehydrogenase bound to the ubiqui surrogate DCIP · the same entry in another collection · chain A against A, TM-score 1.00
- P0A7E1 · AlphaFold monomer V2.0 prediction for dihydroorotate dehydrogenase (quinone) (P0A7E1) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P0A7E1
- Elsewhere: RCSB PDB 7T6C · PDBe 7T6C · UniProt P0A7E1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.