Research workbench
Crystal structure of dehaloperoxidase B in complex with 2,6- dibromophenol
Analyse Crystal structure of dehaloperoxidase B in complex with 2,6- dibromophenol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M1J
- Type
- protein
- Length
- 274 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dehaloperoxidase B
- UniProt
- Q9NAV7
- Ligands
- HEM, 94N, SO4
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 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
- 94N · 2,6-bis(bromanyl)phenol · ligand · chains B
- SO4 · Sulfate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.71 | 0.87 | 24 | HEM, 94N |
| 2 | 150 | 0.69 | 0.88 | 21 | HEM |
Interfaces
1 interface between chains.
- A–B · 497 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7M1J · Crystal structure of dehaloperoxidase B in complex with 2,6-dibromophenol · 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 7M1J · PDBe 7M1J · UniProt Q9NAV7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.