Research workbench
Crystal structure of halotag (M175C) complexed with dansyl-PEG2- halotag ligand
Analyse Crystal structure of halotag (M175C) complexed with dansyl-PEG2- halotag ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y2Y
- Type
- protein
- Length
- 583 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Haloalkane dehalogenase
- EC
- 3.8.1.5
- UniProt
- P0A3G3
- Ligands
- 8LL, CL
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Haloalkane dehalogenase (EC 3.8.1.5) | protein | 291 | 46% helix, 20% strand | P0A3G3 |
| B | Haloalkane dehalogenase (EC 3.8.1.5) | protein | 292 | 46% helix, 20% strand | P0A3G3 |
Ligands and binding sites
- 8LL · 5-(dimethylamino)-~{N}-[2-(2-hexoxyethoxy) ethyl]naphthalene-1-sulfonamide · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 892 | 0.81 | 0.83 | 87 | 8LL, CL |
| 2 | 146 | 0.47 | 0.77 | 24 | empty |
| 3 | 50 | 0.38 | 0.81 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 518 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5Y2Y · Crystal structure of HaloTag (M175C) complexed with dansyl-PEG2-HaloTag ligand · 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 A against A, TM-score 0.99
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 5Y2Y · PDBe 5Y2Y · UniProt P0A3G3
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