Research workbench
HaloTag Engineering for Enhanced Fluorogenicity and Kinetics with a Styrylpyridine Dye
Analyse HaloTag Engineering for Enhanced Fluorogenicity and Kinetics with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OND
- Type
- protein
- Length
- 592 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.45
- Source
- Rhodococcus sp.
- Molecule
- Haloalkane dehalogenase
- EC
- 3.8.1.5
- UniProt
- P0A3G3
- Ligands
- VF2, MG, CL
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · resolution 1.45 · 1 distinct chain · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Haloalkane dehalogenase (EC 3.8.1.5) | protein | 296 | 45% helix, 19% strand | P0A3G3 |
Ligands and binding sites
- VF2 · 4-[(E)-2-[1-(7-chloranylheptyl)pyridin-1-ium-4-yl]ethenyl]-N,N-dimethyl-aniline · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.67 | 0.84 | 32 | VF2, CL |
| 2 | 230 | 0.67 | 0.84 | 32 | VF2, CL |
| 3 | 194 | 0.46 | 0.74 | 42 | empty |
| 4 | 147 | 0.43 | 0.75 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 401 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7OND · Halotag engineering for enhanced fluorogenicity and kinetics with a styrylpyridine dye · the same entry in another collection · chain A against A, TM-score 1.00
- P0A3G3 · AlphaFold monomer V2.0 prediction for haloalkane dehalogenase (P0A3G3) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P0A3G3
- Elsewhere: RCSB PDB 7OND · PDBe 7OND · UniProt P0A3G3
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