Research workbench
Human TRPM2 ion channel in 1 mM ADPR
Analyse Human TRPM2 ion channel in 1 mM ADPR in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8E6Q
- Type
- protein
- Length
- 5,392 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.4
- Source
- Homo sapiens
- Molecule
- Transient receptor potential cation channel subfamily M member 2
- UniProt
- O94759
- Ligands
- APR
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · resolution 3.4 · 1 distinct chain · 45% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transient receptor potential cation channel subfamily M member 2 | protein | 1348 | 45% helix, 9% strand | O94759 |
Ligands and binding sites
- APR · Adenosine-5-diphosphoribose · ligand · 8 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 | 779 | 0.88 | 0.91 | 99 | empty |
| 2 | 1166 | 0.85 | 0.85 | 106 | empty |
| 3 | 1031 | 0.82 | 0.82 | 82 | empty |
| 4 | 281 | 0.82 | 0.92 | 47 | empty |
| 5 | 856 | 0.81 | 0.83 | 83 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3266 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 3266 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 3243 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 3228 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 37 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- O94759 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain A against A, TM-score 0.89
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 O94759
- Elsewhere: RCSB PDB 8E6Q · PDBe 8E6Q · UniProt O94759
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