Research workbench
Cryo-EM structure of human TPC2 channel in the ligand-bound open state
Analyse Cryo-EM structure of human TPC2 channel in the ligand-bound open state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NQ0
- Type
- protein
- Length
- 1,242 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Two pore calcium channel protein 2
- UniProt
- Q8NHX9
- Ligands
- EUJ
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Two pore calcium channel protein 2 | protein | 621 | 69% helix, 0% strand | Q8NHX9 |
Ligands and binding sites
- EUJ · (2R)-3-{[(S)-hydroxy{[(1s,2r,3r,4s,5s,6r)-2,4,6-trihydroxy-3,5-bis(phosphonooxy) cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctanoate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1200 | 0.84 | 0.84 | 57 | empty |
| 2 | 595 | 0.71 | 0.78 | 58 | empty |
| 3 | 806 | 0.71 | 0.76 | 62 | empty |
| 4 | 582 | 0.69 | 0.78 | 51 | empty |
| 5 | 400 | 0.65 | 0.79 | 42 | empty |
Interfaces
1 interface between chains.
- A–B · 4186 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6NQ0 · Cryo-EM structure of human TPC2 channel in the ligand-bound open state · the same entry in another collection · chain A against A, TM-score 1.00
- Q8NHX9 · AlphaFold monomer V2.0 prediction for two pore calcium channel protein 2 (Q8NHX9) · 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 Q8NHX9
- Elsewhere: RCSB PDB 6NQ0 · PDBe 6NQ0 · UniProt Q8NHX9
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