Research workbench
Crystal structure of human two pore domain potassium ion channel TREK2 (K2P10.1) in complex with norfluoxetine
Analyse Crystal structure of human two pore domain potassium ion channel TREK2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XDK
- Type
- protein
- Length
- 973 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Potassium channel subfamily K member 10
- UniProt
- P57789
- Ligands
- PC1, 408, 405, K
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Potassium channel subfamily K member 10 | protein | 248 | 77% helix, 0% strand | P57789 |
| B | Potassium channel subfamily K member 10 | protein | 251 | 75% helix, 0% strand | P57789 |
| C | Potassium channel subfamily K member 10 | protein | 233 | 79% helix, 0% strand | P57789 |
| D | Potassium channel subfamily K member 10 | protein | 241 | 76% helix, 0% strand | P57789 |
Ligands and binding sites
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 4 copies · chains A, B
- 408 · (3R)-3-phenyl-3-[4-(trifluoromethyl)phenoxy]propan-1-amine · ligand · 4 copies · chains A, B, C, D
- 405 · (3S)-3-phenyl-3-[4-(trifluoromethyl)phenoxy]propan-1-amine · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1150 | 0.75 | 0.78 | 59 | 408, 405 |
| 2 | 946 | 0.73 | 0.77 | 95 | empty |
| 3 | 918 | 0.72 | 0.76 | 82 | empty |
| 4 | 807 | 0.68 | 0.74 | 49 | 408, 405 |
| 5 | 233 | 0.62 | 0.81 | 36 | empty |
Interfaces
2 interfaces between chains.
- A–B · 4877 Ų buried · 49 hydrogen bonds · protein-protein
- C–D · 4358 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4XDK · Crystal structure of human two pore domain potassium ion channel TREK2 (K2P10.1) in… · the same entry in another collection · chain D against D, TM-score 1.00
- P57789 · AlphaFold monomer V2.0 prediction for potassium channel subfamily K member 10 (P57789) · a predicted model of the same protein · chain B 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 P57789
- Elsewhere: RCSB PDB 4XDK · PDBe 4XDK · UniProt P57789
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