Research workbench
X-ray crystal structure of halotag bound to the P1 benzoxadiazole fluorogenic ligand
Analyse X-ray crystal structure of halotag bound to the P1 benzoxadiazole fluorogenic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VNP
- Type
- protein
- Length
- 580 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Haloalkane dehalogenase
- EC
- 3.8.1.5
- UniProt
- P0A3G2
- Ligands
- 9FM, CL
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Haloalkane dehalogenase (EC 3.8.1.5) | protein | 290 | 47% helix, 20% strand | P0A3G2 |
Ligands and binding sites
- 9FM · N-{2-[2-(hexyloxy)ethoxy]ethyl}-N~2~-methyl-N~2~-{[7-(methylamino)-2,1,3-benzoxadiazol-4-yl]sulfonyl}glycinamide · ligand · 2 copies · chains A, 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
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 | 118 | 0.65 | 0.88 | 22 | 9FM, CL |
| 2 | 158 | 0.62 | 0.84 | 29 | 9FM, CL |
| 3 | 133 | 0.37 | 0.73 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 136 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5VNP · X-ray crystal structure of Halotag bound to the P1 benzoxadiazole fluorogenic ligand · the same entry in another collection · chain A against A, TM-score 1.00
- P0A3G2 · AlphaFold monomer V2.0 prediction for haloalkane dehalogenase (P0A3G2) · a predicted model of the same protein · chain B 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 P0A3G2
- Elsewhere: RCSB PDB 5VNP · PDBe 5VNP · UniProt P0A3G2
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