Research workbench
X-ray structure of the haloalkane dehalogenase HALOTAG7 labeled with a chloroalkane-carbopyronine fluorophore substrate
Analyse X-ray structure of the haloalkane dehalogenase HALOTAG7 labeled with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y7B
- Type
- protein
- Length
- 1,465 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Haloalkane dehalogenase
- EC
- 3.8.1.5
- UniProt
- P0A3G3
- Ligands
- OEK, CL
- Pockets
- 17 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Haloalkane dehalogenase (EC 3.8.1.5) | protein | 293 | 45% helix, 19% strand | P0A3G3 |
Ligands and binding sites
- OEK · 4-[2-[2-(6-chloranylhexoxy)ethoxy]ethylcarbamoyl]-2-[3-(dimethylamino)-6-(dimethyl-$l^{4}-azanylidene)-10,10-dimethyl-anthracen-9-yl]benzoic acid · ligand · 5 copies · chains A, B, E, C, D
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.76 | 0.78 | 84 | empty |
| 2 | 101 | 0.71 | 0.93 | 23 | CL |
| 3 | 109 | 0.71 | 0.92 | 25 | CL |
| 4 | 114 | 0.70 | 0.92 | 24 | CL |
| 5 | 109 | 0.70 | 0.92 | 24 | CL |
Interfaces
5 interfaces between chains.
- A–D · 614 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 557 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 486 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 461 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 410 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent (covalent ligand).
Compared structures
- 6Y7B · X-ray structure of the Haloalkane dehalogenase HaloTag7 labeled with a… · the same entry in another collection · chain E against E, 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 0.99
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 6Y7B · PDBe 6Y7B · UniProt P0A3G3
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