Research workbench
Cryo-EM structure of CA2+-bound HSSLO1-BETA4 channel complex
Analyse Cryo-EM structure of CA2+-bound HSSLO1-BETA4 channel complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V22
- Type
- protein
- Length
- 4,380 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calcium-activated potassium channel subunit alpha-1; Calcium-activated potassium channel…
- UniProt
- Q12791, Q86W47
- Ligands
- POV, CLR, NAG, CA, MG, K
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 2 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Calcium-activated potassium channel subunit alpha-1 | protein | 896 | 46% helix, 14% strand | Q12791 |
| E, F, G, H | Calcium-activated potassium channel subunit beta-4 | protein | 199 | 48% helix, 21% strand | Q86W47 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 60 copies · chains A, E, B, D, H, F, C, G
- CLR · Cholesterol · ligand · 16 copies · chains A, E, B, F, C, G, D, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains E, F, G, H
- CA · Calcium ion · metal · 8 copies · chains A, D, B, C
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 4 copies · chains A, B, C, 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 | 908 | 0.78 | 0.81 | 71 | MG |
| 2 | 1174 | 0.77 | 0.79 | 81 | MG |
| 3 | 1180 | 0.77 | 0.79 | 83 | MG |
| 4 | 1177 | 0.77 | 0.79 | 80 | MG |
| 5 | 868 | 0.75 | 0.79 | 77 | POV |
Interfaces
18 interfaces between chains.
- A–B · 2415 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 2410 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2401 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 2400 Ų buried · 22 hydrogen bonds · protein-protein
- B–F · 1074 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 covalent, 16 disulfide, 8 glycan (covalent ligand, disulfide, N-glycosylation).
Compared structures
- 6V22 · Cryo-EM structure of Ca2+-bound hsSlo1-beta4 channel complex · the same entry in another collection · chain H against H, TM-score 1.00
- Q12791 · AlphaFold monomer V2.0 prediction for calcium-activated potassium channel subunit alpha-1… · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q86W47 · AlphaFold monomer V2.0 prediction for calcium-activated potassium channel subunit beta-4… · a predicted model of the same protein · chain E against A, TM-score 0.86
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 Q12791
- Every structure of UniProt Q86W47
- Elsewhere: RCSB PDB 6V22 · PDBe 6V22 · UniProt Q12791 · UniProt Q86W47
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