Research workbench
Crystal structure of dehaloperoxidase B at 1.58 and structural characterization of the ab dimer from amphitrite ornata
Analyse Crystal structure of dehaloperoxidase B at 1.58 and structural characterization… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IXF
- 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, SO4, OXY
- Pockets
- 3 · best druggability 0.69
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
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- OXY · Oxygen molecule · ion · chains A
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 | 268 | 0.69 | 0.83 | 28 | HEM |
| 2 | 196 | 0.67 | 0.85 | 22 | HEM, OXY |
| 3 | 158 | 0.47 | 0.77 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 286 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3IXF · Crystal Structure of Dehaloperoxidase B at 1.58 and Structural Characterization of the AB… · 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 3IXF · PDBe 3IXF · UniProt Q9NAV7
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