Research workbench
Crystal structure of human two pore domain potassium ion channel TREK2 (K2P10.1) in complex with a brominated fluoxetine derivative.
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
- 4XDL
- Type
- protein
- Length
- 1,010 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, 40D, K, CD
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Potassium channel subfamily K member 10 | protein | 261 | 75% helix, 0% strand | P57789 |
| B | Potassium channel subfamily K member 10 | protein | 257 | 74% helix, 0% strand | P57789 |
| C | Potassium channel subfamily K member 10 | protein | 234 | 76% helix, 0% strand | P57789 |
| D | Potassium channel subfamily K member 10 | protein | 258 | 74% helix, 0% strand | P57789 |
Ligands and binding sites
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 4 copies · chains A, D
- 40D · 3-[2-bromanyl-4-(trifluoromethyl)phenoxy]-N-methyl-3-phenyl-propan-1-amine · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 6 copies · chains A, B, C, D
- CD · Cadmium ion · metal · 2 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1065 | 0.76 | 0.78 | 63 | 40D |
| 2 | 913 | 0.75 | 0.78 | 59 | 40D |
| 3 | 1076 | 0.73 | 0.76 | 93 | empty |
| 4 | 886 | 0.71 | 0.76 | 77 | empty |
| 5 | 113 | 0.57 | 0.84 | 28 | empty |
Interfaces
5 interfaces between chains.
- C–D · 5065 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 5047 Ų buried · 50 hydrogen bonds · protein-protein
- A–D · 255 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 17 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 13 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4XDL · 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 C 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 4XDL · PDBe 4XDL · UniProt P57789
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