MolNFT v1 · #145203 · protein
Dehaloperoxidase B in complex with substrate 4-nitroguaiacol
6CH5: “Dehaloperoxidase B in complex with substrate 4-nitroguaiacol”. X-ray diffraction, 3 ligands (HEM, F0M, SO4), 3 pockets (best druggability 0.72). MolNFT v1 #145203 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6CH5
- 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, F0M, 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 B | protein | 137 | 77% helix, 1% strand | Q9NAV7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- F0M · 2-methoxy-4-nitrophenol · ligand · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 3 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
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 | 231 | 0.72 | 0.87 | 26 | HEM, F0M |
| 2 | 164 | 0.67 | 0.86 | 22 | HEM |
| 3 | 153 | 0.44 | 0.75 | 27 | PEG |
Interfaces
1 interface between chains.
- A–B · 257 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6CH5 · Dehaloperoxidase B in complex with substrate 4-Nitroguaiacol · 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 6CH5 · PDBe 6CH5 · UniProt Q9NAV7
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