Research workbench
X-ray crystal structure analysis of the binding site in the ferric and oxyferrous forms of the recombinant heme dehaloperoxidase cloned from amphitrite ornata
Analyse X-ray crystal structure analysis of the binding site in the ferric and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QFK
- Type
- protein
- Length
- 274 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dehaloperoxidase a
- UniProt
- Q9NAV8
- Ligands
- HEM, NH4, SO4
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 76% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dehaloperoxidase a | protein | 137 | 76% helix, 1% strand | Q9NAV8 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- NH4 · Ammonium ion · ion · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 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 | 220 | 0.70 | 0.86 | 23 | HEM |
| 2 | 220 | 0.70 | 0.85 | 28 | HEM |
| 3 | 163 | 0.48 | 0.77 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 276 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2QFK · X-ray Crystal Structure Analysis of the Binding Site in the Ferric and Oxyferrous Forms… · 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 Q9NAV8
- Elsewhere: RCSB PDB 2QFK · PDBe 2QFK · UniProt Q9NAV8
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