Research workbench
Cryo-EM structure of CA2+-bound HSSLO1 channel
Analyse Cryo-EM structure of CA2+-bound HSSLO1 channel in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V38
- Type
- protein
- Length
- 3,496 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calcium-activated potassium channel subunit alpha-1
- UniProt
- Q12791
- Ligands
- POV, CLR, CA, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 1 distinct chain · 46% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Calcium-activated potassium channel subunit alpha-1 | protein | 874 | 46% helix, 11% strand | Q12791 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 32 copies · chains A, B, D, C
- CLR · Cholesterol · ligand · 12 copies · chains A, B, C, D
- CA · Calcium ion · metal · 8 copies · chains A, D, B, C
- MG · Magnesium ion · metal · 4 copies · chains A, D, B, C
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 | 953 | 0.82 | 0.83 | 128 | empty |
| 2 | 939 | 0.81 | 0.83 | 126 | empty |
| 3 | 1164 | 0.78 | 0.80 | 128 | empty |
| 4 | 724 | 0.78 | 0.82 | 90 | empty |
| 5 | 110 | 0.76 | 0.96 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2338 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2320 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 2318 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 2259 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 40 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6V38 · Cryo-EM structure of Ca2+-bound hsSlo1 channel · the same entry in another collection · chain A against A, 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 0.97
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 Q12791
- Elsewhere: RCSB PDB 6V38 · PDBe 6V38 · UniProt Q12791
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