Research workbench
Crystal Structure of Dihydroorotate Dehydrogenase from Helicobacter pylori with bound FMN
Analyse Crystal Structure of Dihydroorotate Dehydrogenase from Helicobacter pylori with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B8S
- Type
- protein
- Length
- 671 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.25
- Source
- Helicobacter pylori (strain G27)
- Molecule
- Dihydroorotate dehydrogenase (quinone)
- EC
- 1.3.5.2
- UniProt
- B5Z6I2
- Ligands
- FMN
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.25 · 2 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase (quinone) (EC 1.3.5.2) | protein | 335 | 45% helix, 18% strand | B5Z6I2 |
| B | Dihydroorotate dehydrogenase (quinone) (EC 1.3.5.2) | protein | 336 | 46% helix, 18% strand | B5Z6I2 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, 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 | 1092 | 0.79 | 0.80 | 116 | FMN |
| 2 | 311 | 0.70 | 0.84 | 44 | FMN |
| 3 | 219 | 0.66 | 0.83 | 28 | PGE |
| 4 | 131 | 0.46 | 0.78 | 23 | empty |
| 5 | 67 | 0.36 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 41 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6B8S · Crystal structure of dihydroorotate dehydrogenase from helicobacter pylori with bound FMN · the same entry in another collection · chain A against A, TM-score 1.00
- B5Z6I2 · AlphaFold monomer V2.0 prediction for dihydroorotate dehydrogenase (quinone) (B5Z6I2) · a predicted model of the same protein · chain B 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 B5Z6I2
- Elsewhere: RCSB PDB 6B8S · PDBe 6B8S · UniProt B5Z6I2
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