Research workbench
Structure of TRPM2 ion channel receptor by single particle electron cryo-microscopy, ADPR/CA2+ bound state
Analyse Structure of TRPM2 ion channel receptor by single particle electron… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DRJ
- Type
- protein
- Length
- 5,064 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transient receptor potential cation channel, subfamily M, member 2
- UniProt
- A0A0R4IN04
- Ligands
- APR, CA
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 1 distinct chain · 49% 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 | 1266 | 49% helix, 9% strand | A0A0R4IN04 |
Ligands and binding sites
- APR · Adenosine-5-diphosphoribose · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 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 | 648 | 0.79 | 0.84 | 56 | empty |
| 2 | 144 | 0.79 | 0.96 | 30 | empty |
| 3 | 643 | 0.79 | 0.84 | 50 | empty |
| 4 | 698 | 0.79 | 0.83 | 61 | empty |
| 5 | 866 | 0.78 | 0.81 | 62 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2316 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 2236 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 2225 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 2169 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 13 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6DRJ · Structure of TRPM2 ion channel receptor by single particle electron cryo-microscopy… · the same entry in another collection · chain A 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 A0A0R4IN04
- Elsewhere: RCSB PDB 6DRJ · PDBe 6DRJ · UniProt A0A0R4IN04
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