Research workbench
X-ray structure of the haloalkane dehalogenase HALOTAG7-P174W labeled with a chloroalkane-tetramethylrhodamine fluorophore substrate
Analyse X-ray structure of the haloalkane dehalogenase HALOTAG7-P174W 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
- 6ZVV
- Type
- protein
- Length
- 1,169 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Haloalkane dehalogenase
- EC
- 3.8.1.5
- UniProt
- P0A3G3
- Ligands
- OEH, CA, CL
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Haloalkane dehalogenase (EC 3.8.1.5) | protein | 293 | 46% helix, 19% strand | P0A3G3 |
| B | Haloalkane dehalogenase (EC 3.8.1.5) | protein | 291 | 47% helix, 20% strand | P0A3G3 |
| D | Haloalkane dehalogenase (EC 3.8.1.5) | protein | 292 | 46% helix, 20% 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 · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · chains B
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1100 | 0.76 | 0.78 | 86 | empty |
| 2 | 102 | 0.72 | 0.94 | 25 | CL |
| 3 | 119 | 0.71 | 0.92 | 28 | OEH, CL |
| 4 | 101 | 0.71 | 0.93 | 25 | CL |
| 5 | 103 | 0.70 | 0.92 | 23 | CL |
Interfaces
5 interfaces between chains.
- A–D · 416 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 343 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 202 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 25 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 21 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6ZVV · X-ray structure of the haloalkane dehalogenase HALOTAG7-P174W labeled with a… · the same entry in another collection · chain D against D, 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 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 P0A3G3
- Elsewhere: RCSB PDB 6ZVV · PDBe 6ZVV · UniProt P0A3G3
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