Research workbench
Structure of Dehaloperoxidase B in Complex with Thymoqui
Analyse Structure of Dehaloperoxidase B in Complex with Thymoqui in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SJG
- Type
- protein
- Length
- 274 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.4
- Source
- Amphitrite ornata
- Molecule
- Dehaloperoxidase B
- UniProt
- Q9NAV7
- Ligands
- 9J9, HEM, 9IX, SO4
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · resolution 1.4 · 1 distinct chain · 74% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dehaloperoxidase B | protein | 137 | 74% helix, 1% strand | Q9NAV7 |
Ligands and binding sites
- 9J9 · (6R)-4-hydroxy-6-methyl-3-(propan-2-yl)cyclohexa-2,4-dien-1-one · ligand · 4 copies · chains A, B
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- 9IX · 2-methyl-5-(propan-2-yl)benzene-1,4-diol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.67 | 0.83 | 25 | HEM, 9J9 |
| 2 | 149 | 0.65 | 0.86 | 21 | HEM |
| 3 | 80 | 0.31 | 0.74 | 18 | GOL |
Interfaces
1 interface between chains.
- A–B · 515 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand, additive adduct).
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 Q9NAV7
- Elsewhere: RCSB PDB 7SJG · PDBe 7SJG · UniProt Q9NAV7
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