Research workbench
Single particle cryo-EM structure of the voltage-gated K+ channel EAG1 3-13 deletion mutant bound to calmodulin (conformation 1)
Analyse Single particle cryo-EM structure of the voltage-gated K+ channel EAG1 3-13… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PBY
- Type
- protein
- Length
- 3,268 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Potassium voltage-gated channel subfamily H member 1; Calmodulin-1
- UniProt
- Q63472, P0DP23
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 2 distinct chains · 55% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Potassium voltage-gated channel subfamily H member 1 | protein | 675 | 54% helix, 13% strand | Q63472 |
| B, D, F, H | Calmodulin-1 | protein | 142 | 59% helix, 1% strand | P0DP23 |
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 | 417 | 0.78 | 0.87 | 62 | empty |
| 2 | 426 | 0.78 | 0.86 | 65 | empty |
| 3 | 435 | 0.78 | 0.86 | 58 | empty |
| 4 | 434 | 0.78 | 0.86 | 62 | empty |
| 5 | 1100 | 0.69 | 0.74 | 109 | empty |
Interfaces
18 interfaces between chains.
- A–G · 3710 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 3707 Ų buried · 31 hydrogen bonds · protein-protein
- C–E · 3706 Ų buried · 32 hydrogen bonds · protein-protein
- E–G · 3699 Ų buried · 30 hydrogen bonds · protein-protein
- D–G · 761 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6PBY · Single particle cryo-EM structure of the voltage-gated K+ channel Eag1 3-13 deletion… · the same entry in another collection · chain G against G, TM-score 1.00
- Q63472 · AlphaFold monomer V2.0 prediction for potassium voltage-gated channel subfamily H member… · a predicted model of the same protein · chain A against A, TM-score 0.98
- P0DP23 · AlphaFold monomer V2.0 prediction for calmodulin-1 (P0DP23) · a predicted model of the same protein · chain D against A, TM-score 0.46
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 Q63472
- Every structure of UniProt P0DP23
- Elsewhere: RCSB PDB 6PBY · PDBe 6PBY · UniProt Q63472 · UniProt P0DP23
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