Research workbench
Cryo-EM structure of CA2+-free HSSLO1-BETA4 channel complex
Analyse Cryo-EM structure of CA2+-free 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
- 6V35
- Type
- protein
- Length
- 4,448 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
- PGW, CLR, NAG
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 2 distinct chains · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Calcium-activated potassium channel subunit alpha-1 | protein | 914 | 43% helix, 12% strand | Q12791 |
| E, F, G, H | Calcium-activated potassium channel subunit beta-4 | protein | 198 | 45% helix, 18% strand | Q86W47 |
Ligands and binding sites
- PGW · (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate · ligand · 40 copies · chains A, E, B, D, H, F, C, G
- CLR · Cholesterol · ligand · 8 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
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 | 867 | 0.79 | 0.81 | 75 | PGW |
| 2 | 663 | 0.78 | 0.83 | 73 | empty |
| 3 | 852 | 0.78 | 0.80 | 93 | PGW |
| 4 | 643 | 0.78 | 0.83 | 69 | empty |
| 5 | 821 | 0.77 | 0.81 | 95 | PGW |
Interfaces
18 interfaces between chains.
- C–D · 1957 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1936 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1923 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1917 Ų buried · 12 hydrogen bonds · protein-protein
- A–E · 1057 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 8 covalent, 8 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 6V35 · Cryo-EM structure of Ca2+-free 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 0.94
- 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 6V35 · PDBe 6V35 · UniProt Q12791 · UniProt Q86W47
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