MolNFT v1 · #163182 · protein
Crystal structure of the human two pore domain potassium ion channel task-1 (K2P3.1) in a closed conformation with a bound inhibitor bay 1000493
6RV3 · Potassium channel subfamily K member 3: “Crystal structure of the human two pore domain potassium ion channel task-1 (K2P3.1) in a closed conformation…”. X-ray diffraction, 4 ligands (Y01, PC1, KKQ), 9 pockets (best druggability…
- PDB
- 6RV3
- Type
- protein
- Length
- 1,036 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Potassium channel subfamily K member 3
- UniProt
- O14649
- Ligands
- Y01, PC1, KKQ, K
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Potassium channel subfamily K member 3 | protein | 258 | 79% helix, 0% strand | O14649 |
| B | Potassium channel subfamily K member 3 | protein | 259 | 79% helix, 0% strand | O14649 |
| C | Potassium channel subfamily K member 3 | protein | 258 | 78% helix, 0% strand | O14649 |
| D | Potassium channel subfamily K member 3 | protein | 261 | 79% helix, 0% strand | O14649 |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · 7 copies · chains A, B, C, D
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 3 copies · chains A, B, C, D
- KKQ · [4-[[2-(4-bromophenyl)imidazo[1,2-a]pyridin-3-yl]methyl]piperazin-1-yl]-(2-fluorophenyl)methanone · ligand · 2 copies · chains A, B, C, D
- K · Potassium ion · metal · 8 copies · chains A, B, C, D
- DMU · Decyl-beta-D-maltopyranoside · additive · 4 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.85 | 0.87 | 75 | Y01, KKQ |
| 2 | 879 | 0.84 | 0.86 | 80 | Y01, KKQ |
| 3 | 990 | 0.71 | 0.75 | 64 | empty |
| 4 | 961 | 0.70 | 0.75 | 66 | empty |
| 5 | 118 | 0.41 | 0.76 | 16 | empty |
Interfaces
4 interfaces between chains.
- C–D · 5652 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 5577 Ų buried · 48 hydrogen bonds · protein-protein
- A–C · 44 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 29 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6RV3 · Crystal structure of the human two pore domain potassium ion channel TASK-1 (K2P3.1) in a… · the same entry in another collection · chain D against D, TM-score 1.00
- O14649 · AlphaFold monomer V2.0 prediction for potassium channel subfamily K member 3 (O14649) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O14649
- Elsewhere: RCSB PDB 6RV3 · PDBe 6RV3 · UniProt O14649
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