Research workbench
Cryo-EM structure of the hyperpolarization-activated potassium channel KAT1: octamer
Analyse Cryo-EM structure of the hyperpolarization-activated potassium channel KAT1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V1Y
- Type
- protein
- Length
- 3,568 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Potassium channel KAT1
- UniProt
- Q39128
- Ligands
- QNP, QNJ
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 1 distinct chain · 57% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, M, N, O, P | Potassium channel KAT1 | protein | 446 | 57% helix, 6% strand | Q39128 |
Ligands and binding sites
- QNP · (2S)-1-(nonanoyloxy)-3-(phosphonooxy)propan-2-yl tetradecanoate · ligand · 8 copies · chains A, B, C, D, M, N, O, P
- QNJ · (3beta,5beta,14beta,17alpha)-cholestan-3-ol · ligand · 8 copies · chains A, B, C, D, M, N, O, P
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 | 241 | 0.82 | 0.94 | 44 | empty |
| 2 | 251 | 0.82 | 0.94 | 48 | empty |
| 3 | 941 | 0.77 | 0.79 | 103 | empty |
| 4 | 923 | 0.76 | 0.79 | 110 | empty |
| 5 | 609 | 0.73 | 0.80 | 70 | empty |
Interfaces
16 interfaces between chains.
- A–D · 2462 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 2460 Ų buried · 15 hydrogen bonds · protein-protein
- M–P · 2456 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 2453 Ų buried · 14 hydrogen bonds · protein-protein
- N–O · 2453 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6V1Y · Cryo-EM Structure of the Hyperpolarization-Activated Potassium Channel KAT1: Octamer · the same entry in another collection · chain P against P, TM-score 1.00
- Q39128 · AlphaFold monomer V2.0 prediction for potassium channel KAT1 (Q39128) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q39128
- Elsewhere: RCSB PDB 6V1Y · PDBe 6V1Y · UniProt Q39128
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