MolNFT v1 · #172228 · protein
X-ray structure of the haloalkane dehalogenase HALOTAG7-Q165H labeled with a chloroalkane-tetramethylrhodamine fluorophore substrate
6ZVW: “X-ray structure of the haloalkane dehalogenase HALOTAG7-Q165H labeled with a…”. X-ray diffraction, 2 ligands (OEH, CL), 3 pockets (best druggability 0.75). MolNFT v1 #172228 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6ZVW
- Type
- protein
- Length
- 586 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
- OEH, CL
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Haloalkane dehalogenase (EC 3.8.1.5) | protein | 293 | 46% helix, 19% strand | P0A3G3 |
Ligands and binding sites
- OEH · [9-[2-carboxy-5-[2-[2-(6-chloranylhexoxy) ethoxy]ethylcarbamoyl]phenyl]-6-(dimethylamino) xanthen-3-ylidene]-dimethyl-azanium · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains 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 | 689 | 0.75 | 0.80 | 74 | OEH, CL, GOL |
| 2 | 98 | 0.71 | 0.93 | 25 | CL |
| 3 | 50 | 0.34 | 0.78 | 11 | PEG |
Interfaces
1 interface between chains.
- A–B · 396 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6ZVW · X-ray structure of the haloalkane dehalogenase HALOTAG7-Q165H labeled with a… · 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 6ZVW · PDBe 6ZVW · UniProt P0A3G3
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