Research workbench
The V59W mutation blocks the distal pocket of the hemoglobin - dehaloperoxidase from amphitrite ornata
Analyse The V59W mutation blocks the distal pocket of the hemoglobin - dehaloperoxidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O7N
- 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, BML, SO4
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 77% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dehaloperoxidase a | protein | 137 | 77% helix, 1% strand | Q9NAV8 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- BML · 4-bromophenol · ligand · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.68 | 0.85 | 27 | HEM |
| 2 | 213 | 0.67 | 0.84 | 28 | HEM, BML |
| 3 | 150 | 0.52 | 0.80 | 21 | SO4 |
Interfaces
1 interface between chains.
- A–B · 368 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3O7N · The V59W mutation blocks the distal pocket of the hemoglobin - dehaloperoxidase from… · 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 3O7N · PDBe 3O7N · UniProt Q9NAV8
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