MolNFT v1 · #108711 · protein
Human traak K+ channel in a tl+ bound nonconductive conformation
4WFH · Potassium channel subfamily K member 4: “Human traak K+ channel in a tl+ bound nonconductive conformation”. X-ray diffraction, 3 ligands (D10, TL, CA), 19 pockets (best druggability 0.71). MolNFT v1 #108711 on GenesisL1: 3D…
- PDB
- 4WFH
- Type
- protein
- Length
- 1,339 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Potassium channel subfamily K member 4; Anti-traak antibody 13E9 Fab fragment light…
- UniProt
- Q9NYG8
- Ligands
- D10, TL, CA
- Pockets
- 19 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 37% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Potassium channel subfamily K member 4 | protein | 253 | 76% helix, 1% strand | Q9NYG8 |
| B | Potassium channel subfamily K member 4 | protein | 243 | 75% helix, 0% strand | Q9NYG8 |
| D, F | Anti-traak antibody 13E9 Fab fragment light chain | protein | 211 | 6% helix, 51% strand | — |
| E | Anti-traak antibody 13E9 Fab fragment heavy chain | protein | 211 | 7% helix, 51% strand | — |
| G | Anti-traak antibody 13E9 Fab fragment heavy chain | protein | 210 | 7% helix, 52% strand | — |
Ligands and binding sites
- D10 · Decane · ligand · chains A, B
- TL · Thallium (I) ion · metal · 7 copies · chains A, B
- CA · Calcium ion · metal · 3 copies · chains A, B, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 946 | 0.71 | 0.76 | 90 | TL |
| 2 | 175 | 0.70 | 0.87 | 20 | empty |
| 3 | 689 | 0.69 | 0.76 | 54 | D10 |
| 4 | 438 | 0.59 | 0.75 | 57 | empty |
| 5 | 394 | 0.57 | 0.75 | 55 | empty |
Interfaces
12 interfaces between chains.
- A–B · 5127 Ų buried · 42 hydrogen bonds · protein-protein
- D–E · 1736 Ų buried · 15 hydrogen bonds · protein-protein
- F–G · 1723 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 472 Ų buried · 8 hydrogen bonds · protein-protein
- B–G · 466 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 4WFH · Human TRAAK K+ channel in a Tl+ bound nonconductive conformation · the same entry in another collection · chain G against G, TM-score 1.00
- Q9NYG8 · AlphaFold monomer V2.0 prediction for potassium channel subfamily K member 4 (Q9NYG8) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q9NYG8
- Elsewhere: RCSB PDB 4WFH · PDBe 4WFH · UniProt Q9NYG8
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