Research workbench
Crystal structure of dehaloperoxidase B in complex with cofactor IRON(III) deuteroporphyrin IX and substrate 4-nitrophenol
Analyse Crystal structure of dehaloperoxidase B in complex with cofactor IRON(III)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VDT
- 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
- FDE, NPO, SO4
- Pockets
- 2 · best druggability 0.67
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
- FDE · Fe(iii) deuteroporphyrin IX · ligand · 2 copies · chains A, B
- NPO · P-nitrophenol · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
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 | 254 | 0.67 | 0.83 | 31 | FDE, NPO |
| 2 | 244 | 0.65 | 0.82 | 30 | FDE |
Interfaces
1 interface between chains.
- A–B · 524 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6VDT · Crystal Structure of Dehaloperoxidase B in Complex with cofactor Iron(III)… · 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 6VDT · PDBe 6VDT · UniProt Q9NAV7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.