Research workbench
Cryo-EM structure of AKT1-AtKC1
Analyse Cryo-EM structure of AKT1-AtKC1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WM1
- Type
- protein
- Length
- 1,844 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Arabidopsis thaliana
- Molecule
- Potassium channel AKT1; Potassium channel KAT3
- UniProt
- Q38998, P92960
- Ligands
- POV, K
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · resolution 2.8 · 2 distinct chains · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Potassium channel AKT1 | protein | 449 | 51% helix, 10% strand | Q38998 |
| B, D | Potassium channel KAT3 | protein | 473 | 48% helix, 9% strand | P92960 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 4 copies · chains A, D, B, C
- K · Potassium ion · metal · 3 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.85 | 0.92 | 55 | empty |
| 2 | 1078 | 0.76 | 0.78 | 96 | empty |
| 3 | 1097 | 0.75 | 0.78 | 99 | empty |
| 4 | 548 | 0.68 | 0.78 | 48 | empty |
| 5 | 421 | 0.67 | 0.79 | 27 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3036 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 3004 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 2173 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 2167 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 384 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- Q38998 · AlphaFold monomer V2.0 prediction for potassium channel AKT1 (Q38998) · a predicted model of the same protein · chain C against A, TM-score 0.84
- P92960 · AlphaFold monomer V2.0 prediction for potassium channel KAT3 (P92960) · a predicted model of the same protein · chain D against A, TM-score 0.81
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 Q38998
- Every structure of UniProt P92960
- Elsewhere: RCSB PDB 7WM1 · PDBe 7WM1 · UniProt Q38998 · UniProt P92960
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