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Crystal Structure of Rat TRPV6*-Y466A- in complex with brominated 2-Aminoethoxydiphenyl borate (2-APB-Br)
Analyse Crystal Structure of Rat TRPV6*-Y466A- in complex with brominated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D7X
- Type
- protein
- Length
- 600 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.6
- Source
- Rattus norvegicus
- Molecule
- Transient receptor potential cation channel subfamily V member 6
- UniProt
- Q9R186
- Ligands
- FYY, DTB, CA
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · resolution 3.6 · 1 distinct chain · 54% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transient receptor potential cation channel subfamily V member 6 | protein | 600 | 54% helix, 4% strand | Q9R186 |
Ligands and binding sites
- FYY · 2-aminoethyl (4-bromophenyl)phenylborinate · ligand · chains A
- DTB · 6-(5-methyl-2-oxo-imidazolidin-4-yl)-hexanoic acid · ligand · chains A
- CA · Calcium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 690 | 0.73 | 0.79 | 57 | FYY |
| 2 | 136 | 0.65 | 0.87 | 20 | empty |
| 3 | 186 | 0.55 | 0.79 | 28 | DTB |
| 4 | 93 | 0.49 | 0.82 | 13 | empty |
| 5 | 102 | 0.38 | 0.75 | 18 | empty |
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 6D7X · Crystal structure of rat TRPV6*-Y466A- in complex with brominated 2- aminoethoxydiphenyl… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9R186 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9R186
- Elsewhere: RCSB PDB 6D7X · PDBe 6D7X · UniProt Q9R186
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