Research workbench
Crystal structure of dehaloperoxidase B in complex with p-cymene
Analyse Crystal structure of dehaloperoxidase B in complex with p-cymene in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SJE
- Type
- protein
- Length
- 274 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.72
- Source
- Amphitrite ornata
- Molecule
- Dehaloperoxidase B
- UniProt
- Q9NAV7
- Ligands
- HEM, MML, SO4, OXY
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · resolution 1.72 · 1 distinct chain · 77% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dehaloperoxidase B | protein | 137 | 77% helix, 1% strand | Q9NAV7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- MML · 1-methyl-4-(1-methylethyl)benzene · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
- OXY · Oxygen molecule · ion · chains 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 | 264 | 0.70 | 0.84 | 26 | HEM, MML |
| 2 | 245 | 0.68 | 0.84 | 26 | HEM, OXY, MML |
| 3 | 65 | 0.27 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 520 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
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 7SJE · PDBe 7SJE · UniProt Q9NAV7
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