Research workbench
Human traak K+ channel in a tl+ bound conductive conformation
Analyse Human traak K+ channel in a tl+ bound conductive conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WFG
- Type
- protein
- Length
- 1,351 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
- TL, CA
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 38% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Potassium channel subfamily K member 4 | protein | 253 | 76% helix, 0% strand | Q9NYG8 |
| B | Potassium channel subfamily K member 4 | protein | 255 | 76% helix, 1% strand | Q9NYG8 |
| D, F | Anti-traak antibody 13E9 Fab fragment light chain | protein | 211 | 7% 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
- TL · Thallium (I) ion · metal · 8 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
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 848 | 0.75 | 0.79 | 59 | TL |
| 2 | 180 | 0.70 | 0.87 | 20 | empty |
| 3 | 158 | 0.70 | 0.88 | 20 | empty |
| 4 | 707 | 0.67 | 0.76 | 83 | TL |
| 5 | 439 | 0.58 | 0.75 | 58 | empty |
Interfaces
12 interfaces between chains.
- A–B · 5366 Ų buried · 44 hydrogen bonds · protein-protein
- D–E · 1732 Ų buried · 14 hydrogen bonds · protein-protein
- F–G · 1723 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 470 Ų buried · 8 hydrogen bonds · protein-protein
- B–G · 467 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 4WFG · Human TRAAK K+ channel in a Tl+ bound conductive 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 0.94
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 4WFG · PDBe 4WFG · UniProt Q9NYG8
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