MolNFT v1 · #167215 · protein
Crystal structure of dehaloperoxidase B wild type in complex with substrate trichlorophenol
6VDY: “Crystal structure of dehaloperoxidase B wild type in complex with substrate trichlorophenol”. X-ray diffraction, 3 ligands (HEM, T6C, SO4), 2 pockets (best druggability 0.70). MolNFT v1 #167215 on GenesisL1: 3D structure, binding…
- PDB
- 6VDY
- 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, T6C, SO4
- Pockets
- 2 · best druggability 0.70
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
- T6C · 2,4,6-trichlorophenol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · 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 | 275 | 0.70 | 0.84 | 29 | HEM, T6C |
| 2 | 293 | 0.67 | 0.82 | 35 | HEM, T6C |
Interfaces
1 interface between chains.
- A–B · 486 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6VDY · Crystal Structure of Dehaloperoxidase B wild type in Complex with Substrate… · 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 6VDY · PDBe 6VDY · UniProt Q9NAV7
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