MolNFT v1 · #160454 · protein
Cryo-EM structure of the zebrafish TRPM2 channel in the presence of adpr and CA2+
6PKX · Transient receptor potential cation channel subfamily M…: “Cryo-EM structure of the zebrafish TRPM2 channel in the presence of adpr and CA2+”. Electron microscopy, 2 ligands (AR6, CA), 20 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 6PKX
- Type
- protein
- Length
- 4,848 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transient receptor potential cation channel subfamily M member 2
- Ligands
- AR6, CA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 53% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Transient receptor potential cation channel subfamily M member 2 | protein | 1206 | 52% helix, 7% strand | — |
| B, D | Transient receptor potential cation channel subfamily M member 2 | protein | 1218 | 53% helix, 7% strand | — |
Ligands and binding sites
- AR6 · [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2R,3S,4R,5S)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate · ligand · 2 copies · chains B, D
- CA · Calcium ion · metal · 2 copies · chains B, 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 | 959 | 0.84 | 0.84 | 115 | empty |
| 2 | 805 | 0.82 | 0.84 | 86 | empty |
| 3 | 604 | 0.79 | 0.85 | 69 | empty |
| 4 | 544 | 0.78 | 0.84 | 82 | empty |
| 5 | 168 | 0.78 | 0.93 | 25 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2407 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 2395 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 1749 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 1746 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 91 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6PKX · Cryo-EM structure of the zebrafish TRPM2 channel in the presence of ADPR and Ca2+ · 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
- Elsewhere: RCSB PDB 6PKX · PDBe 6PKX
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