Research workbench
K2P2.1(TREK-1)I110D:RUR:ML335 bound channel structure
Analyse K2P2.1(TREK-1)I110D:RUR:ML335 bound channel structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V37
- Type
- protein
- Length
- 534 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Potassium channel subfamily K member 2
- Ligands
- D12, Q6F, R2R, K, CD
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Potassium channel subfamily K member 2 | protein | 263 | 75% helix, 0% strand | — |
| B | Potassium channel subfamily K member 2 | protein | 271 | 77% helix, 0% strand | — |
Ligands and binding sites
- D12 · Dodecane · ligand · 4 copies · chains A, B
- Q6F · N-[(2,4-dichlorophenyl)methyl]-4-[(methylsulfonyl) amino]benzamide · ligand · 2 copies · chains A, B
- R2R · ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2) · ligand · chains A, B
- K · Potassium ion · metal · 5 copies · chains A, B
- CD · Cadmium ion · metal · 3 copies · chains A, B
- HEX · Hexane · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1093 | 0.80 | 0.81 | 131 | R2R, Q6F |
| 2 | 551 | 0.65 | 0.76 | 40 | K |
| 3 | 52 | 0.53 | 0.89 | 17 | empty |
| 4 | 87 | 0.49 | 0.82 | 19 | empty |
| 5 | 88 | 0.41 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 4890 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6V37 · K2P2.1(TREK-1)I110D:RuR:ML335 bound channel structure · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 6V37 · PDBe 6V37
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