Research workbench
Dehaloperoxidase B in complex with substrate 4-methyl-cresol
Analyse Dehaloperoxidase B in complex with substrate 4-methyl-cresol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ONR
- Type
- protein
- Length
- 274 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.35
- Source
- Amphitrite ornata
- Molecule
- Dehaloperoxidase B
- UniProt
- Q9NAV7
- Ligands
- HEM, N0D, SO4
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · resolution 1.35 · 1 distinct chain · 76% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dehaloperoxidase B | protein | 137 | 76% helix, 1% strand | Q9NAV7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- N0D · 2,4-dimethylphenol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 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 | 321 | 0.72 | 0.84 | 33 | HEM, N0D |
| 2 | 303 | 0.70 | 0.83 | 29 | HEM, N0D |
| 3 | 54 | 0.27 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 518 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6ONR · Dehaloperoxidase B in complex with substrate 4-methyl-cresol · 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 Q9NAV7
- Elsewhere: RCSB PDB 6ONR · PDBe 6ONR · UniProt Q9NAV7
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