Research workbench
calcium channel-ligand
Analyse calcium channel-ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KZP
- Type
- protein
- Length
- 1,014 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.1
- Source
- Homo sapiens
- Molecule
- Voltage-dependent T-type calcium channel subunit alpha-1G,Voltage-dependent T-type…
- UniProt
- O43497
- Ligands
- 3PE, Y01, DZR, NAG, CA
- Pockets
- 19 · best druggability 0.84
Structure
electron microscopy · resolution 3.1 · 1 distinct chain · 71% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Voltage-dependent T-type calcium channel subunit alpha-1G,Voltage-dependent T-type calcium channel subunit alpha-1G | protein | 1014 | 71% helix, 2% strand | O43497 |
Ligands and binding sites
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 8 copies · chains A
- Y01 · Cholesterol hemisuccinate · ligand · 3 copies · chains A
- DZR · ~{N}-[[1-[2-(~{tert}-butylamino)-2-oxidanylidene-ethyl]piperidin-4-yl]methyl]-3-chloranyl-5-fluoranyl-benzamide · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- CA · Calcium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1133 | 0.84 | 0.85 | 83 | CA, DZR, 3PE |
| 2 | 696 | 0.67 | 0.76 | 70 | empty |
| 3 | 331 | 0.67 | 0.81 | 40 | empty |
| 4 | 288 | 0.64 | 0.81 | 30 | empty |
| 5 | 284 | 0.60 | 0.78 | 31 | 3PE |
Modifications
Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
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 O43497
- Elsewhere: RCSB PDB 6KZP · PDBe 6KZP · UniProt O43497
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