MolNFT v1 · #152100 · protein
Dehaloperoxidase B from amphitrite ornata - complex with 2,4- dichlorophenol
6I7F: “Dehaloperoxidase B from amphitrite ornata - complex with 2,4- dichlorophenol”. X-ray diffraction, 3 ligands (HEM, 5JC, SO4), 2 pockets (best druggability 0.75). MolNFT v1 #152100 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6I7F
- 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, 5JC, SO4
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dehaloperoxidase B | protein | 137 | 74% helix, 1% strand | Q9NAV7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- 5JC · 2,4-dichlorophenol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
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 | 255 | 0.75 | 0.88 | 27 | HEM, 5JC |
| 2 | 242 | 0.72 | 0.86 | 26 | HEM, 5JC |
Interfaces
1 interface between chains.
- A–B · 496 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6I7F · Dehaloperoxidase B from Amphitrite ornata - complex with 2,4-dichlorophenol · 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 6I7F · PDBe 6I7F · UniProt Q9NAV7
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