Research workbench
Cryo-EM structure of mouse TPC1 channel in the PTDINS(3,5)P2-bound state
Analyse Cryo-EM structure of mouse TPC1 channel in the PTDINS(3,5)P2-bound state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C9A
- Type
- protein
- Length
- 1,446 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Two pore calcium channel protein 1
- UniProt
- Q9EQJ0
- Ligands
- EUJ, NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 68% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Two pore calcium channel protein 1 | protein | 723 | 68% helix, 3% strand | Q9EQJ0 |
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 B, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1077 | 0.84 | 0.85 | 60 | empty |
| 2 | 750 | 0.78 | 0.82 | 72 | empty |
| 3 | 728 | 0.78 | 0.82 | 70 | empty |
| 4 | 927 | 0.73 | 0.77 | 69 | empty |
| 5 | 556 | 0.68 | 0.77 | 54 | empty |
Interfaces
1 interface between chains.
- B–A · 3692 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan (N-glycosylation).
Compared structures
- 6C9A · Cryo-EM structure of mouse TPC1 channel in the PtdIns(3,5)P2-bound state · the same entry in another collection · chain B against B, TM-score 1.00
- Q9EQJ0 · AlphaFold monomer V2.0 prediction for two pore calcium channel protein 1 (Q9EQJ0) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q9EQJ0
- Elsewhere: RCSB PDB 6C9A · PDBe 6C9A · UniProt Q9EQJ0
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