Research workbench
K2P2.1(TREK-1)I110D:RU360 bound channel structure
Analyse K2P2.1(TREK-1)I110D:RU360 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
- 6V3C
- Type
- protein
- Length
- 510 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Potassium channel subfamily K member 2
- Ligands
- RU3, LNK, K, CD
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Potassium channel subfamily K member 2 | protein | 250 | 78% helix, 0% strand | — |
| B | Potassium channel subfamily K member 2 | protein | 260 | 75% helix, 0% strand | — |
Ligands and binding sites
- RU3 · ruthenium(6+) formate azanide tetraamino(formato-kappaO)oxidoruthenate(1-) (1/1/4/1) · ligand · chains A, B
- LNK · Pentane · ligand · chains A
- K · Potassium ion · metal · 5 copies · chains A, B
- CD · Cadmium ion · metal · 3 copies · chains A, B
- OCT · N-octane · additive · 4 copies · chains A, B
- HEX · Hexane · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1158 | 0.72 | 0.76 | 95 | RU3, CD |
| 2 | 167 | 0.69 | 0.88 | 34 | empty |
| 3 | 547 | 0.65 | 0.76 | 41 | K |
| 4 | 134 | 0.45 | 0.76 | 23 | empty |
| 5 | 113 | 0.40 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 4910 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6V3C · K2P2.1(TREK-1)I110D:Ru360 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 6V3C · PDBe 6V3C
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