MolNFT v1 · #109803 · protein
Crystal structure of human two pore domain potassium ion channel TREK2 (K2P10.1) in an alternate conformation (form 2)
4XDJ · Potassium channel subfamily K member 10: “Crystal structure of human two pore domain potassium ion channel TREK2 (K2P10.1) in an alternate conformation…”. X-ray diffraction, 3 ligands (PC1, TRD, K), 13 pockets (best druggability…
- PDB
- 4XDJ
- Type
- protein
- Length
- 961 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, TRD, K
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Potassium channel subfamily K member 10 | protein | 251 | 76% helix, 0% strand | P57789 |
| B | Potassium channel subfamily K member 10 | protein | 243 | 78% helix, 0% strand | P57789 |
| C | Potassium channel subfamily K member 10 | protein | 224 | 77% helix, 0% strand | P57789 |
| D | Potassium channel subfamily K member 10 | protein | 243 | 80% helix, 0% strand | P57789 |
Ligands and binding sites
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 4 copies · chains A, B
- TRD · Tridecane · 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
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1153 | 0.76 | 0.78 | 67 | TRD |
| 2 | 1033 | 0.72 | 0.76 | 64 | TRD |
| 3 | 718 | 0.68 | 0.76 | 69 | empty |
| 4 | 476 | 0.60 | 0.75 | 49 | empty |
| 5 | 84 | 0.44 | 0.80 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 5105 Ų buried · 51 hydrogen bonds · protein-protein
- C–D · 4598 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4XDJ · Crystal structure of human two pore domain potassium ion channel TREK2 (K2P10.1) in an… · the same entry in another collection · chain C against C, 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 0.97
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 4XDJ · PDBe 4XDJ · UniProt P57789
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