Research workbench
Cryo-EM structure of human TRPV6-Y467A in complex with 2- aminoethoxydiphenyl borate (2-apb)
Analyse Cryo-EM structure of human TRPV6-Y467A in complex with 2- aminoethoxydiphenyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D7T
- Type
- protein
- Length
- 2,444 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transient receptor potential cation channel subfamily V member 6
- UniProt
- Q9H1D0
- Ligands
- FZ4, CA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 51% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transient receptor potential cation channel subfamily V member 6 | protein | 611 | 51% helix, 4% strand | Q9H1D0 |
Ligands and binding sites
- FZ4 · 2-aminoethyl diphenylborinate · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.85 | 0.94 | 36 | empty |
| 2 | 540 | 0.79 | 0.85 | 45 | FZ4 |
| 3 | 625 | 0.79 | 0.84 | 48 | FZ4 |
| 4 | 634 | 0.78 | 0.83 | 47 | FZ4 |
| 5 | 544 | 0.78 | 0.85 | 43 | FZ4 |
Interfaces
6 interfaces between chains.
- B–C · 3654 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 3645 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 3641 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 3639 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 59 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6D7T · Cryo-EM structure of human TRPV6-Y467A in complex with 2-Aminoethoxydiphenyl borate… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H1D0 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9H1D0
- Elsewhere: RCSB PDB 6D7T · PDBe 6D7T · UniProt Q9H1D0
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