MolNFT v1 · #145422 · protein
Cryo-EM structure of the human SK4/CALMODULIN channel complex
6CNM · Intermediate conductance calcium-activated potassium…: “Cryo-EM structure of the human SK4/CALMODULIN channel complex”. Electron microscopy, 2 ligands (POV, K), 20 pockets (best druggability 0.82). MolNFT v1 #145422 on GenesisL1: 3D…
- PDB
- 6CNM
- Type
- protein
- Length
- 1,700 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Intermediate conductance calcium-activated potassium channel protein 4; Calmodulin-1
- UniProt
- O15554, P0DP23
- Ligands
- POV, K
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 2 distinct chains · 74% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Intermediate conductance calcium-activated potassium channel protein 4 | protein | 359 | 77% helix, 0% strand | O15554 |
| E, F, G, H | Calmodulin-1 | protein | 66 | 56% helix, 9% strand | P0DP23 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 4 copies · chains D, A, B, C
- K · Potassium ion · metal · 5 copies · chains A, B, C, D
- LMT · Dodecyl-beta-D-maltoside · additive · 8 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.82 | 0.95 | 30 | empty |
| 2 | 360 | 0.73 | 0.84 | 44 | empty |
| 3 | 356 | 0.73 | 0.85 | 42 | empty |
| 4 | 383 | 0.72 | 0.83 | 44 | empty |
| 5 | 356 | 0.70 | 0.82 | 39 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1390 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 1386 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1385 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 1384 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 840 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (additive adduct).
Compared structures
- 6CNM · Cryo-EM structure of the human SK4/calmodulin channel complex · the same entry in another collection · chain H against H, TM-score 1.00
- O15554 · AlphaFold monomer V2.0 prediction for intermediate conductance calcium-activated… · a predicted model of the same protein · chain A against A, TM-score 0.91
- P0DP23 · AlphaFold monomer V2.0 prediction for calmodulin-1 (P0DP23) · a predicted model of the same protein · chain E against A, TM-score 0.59
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 O15554
- Every structure of UniProt P0DP23
- Elsewhere: RCSB PDB 6CNM · PDBe 6CNM · UniProt O15554 · UniProt P0DP23
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