MolNFT v1 · #144938 · protein
Cryo-EM structure of mouse TPC1 channel in the apo state
6C96 · Two pore calcium channel protein 1: “Cryo-EM structure of mouse TPC1 channel in the apo state”. Electron microscopy, 2 ligands (NAG, NA), 20 pockets (best druggability 0.85). MolNFT v1 #144938 on GenesisL1: 3D structure, binding…
- PDB
- 6C96
- 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
- NAG, NA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 67% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Two pore calcium channel protein 1 | protein | 723 | 67% helix, 3% strand | Q9EQJ0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- NA · Sodium ion · metal · 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1130 | 0.85 | 0.86 | 64 | NA |
| 2 | 1054 | 0.75 | 0.78 | 86 | empty |
| 3 | 1094 | 0.75 | 0.78 | 85 | empty |
| 4 | 897 | 0.75 | 0.79 | 67 | empty |
| 5 | 795 | 0.74 | 0.79 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 4364 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan (N-glycosylation).
Compared structures
- 6C96 · Cryo-EM structure of mouse TPC1 channel in the apo state · the same entry in another collection · chain A against A, 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 A 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 6C96 · PDBe 6C96 · UniProt Q9EQJ0
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