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Structure of the L100F mutant of dehaloperoxidase-hemoglobin a from amphitrite ornata with 4-bromophenol
Analyse Structure of the L100F mutant of dehaloperoxidase-hemoglobin a from amphitrite… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HSX
- Type
- protein
- Length
- 274 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dehaloperoxidase a
- EC
- 1.11.1.7
- UniProt
- Q9NAV8
- Ligands
- HEM, BML, SO4
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 77% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dehaloperoxidase a (EC 1.11.1.7) | 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 · 4 copies · chains A, B
- GOL · Glycerol · additive · 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 | 316 | 0.72 | 0.84 | 27 | HEM, BML |
| 2 | 274 | 0.68 | 0.83 | 31 | HEM |
| 3 | 124 | 0.37 | 0.73 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 231 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4HSX · Structure of the L100F mutant of dehaloperoxidase-hemoglobin A from Amphitrite ornata… · 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 4HSX · PDBe 4HSX · UniProt Q9NAV8
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