MolNFT v1 · #166866 · protein
K2P2.1(TREK-1)I110D:RUR bound channel structure
6V3I · Potassium channel subfamily K member 2: “K2P2.1(TREK-1)I110D:RUR bound channel structure”. X-ray diffraction, 5 ligands (D12, R2R, LNK), 16 pockets (best druggability 0.73). MolNFT v1 #166866 on GenesisL1: 3D structure, binding…
- PDB
- 6V3I
- Type
- protein
- Length
- 525 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Potassium channel subfamily K member 2
- Ligands
- D12, R2R, LNK, K, CD
- Pockets
- 16 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Potassium channel subfamily K member 2 | protein | 252 | 83% helix, 0% strand | — |
| B | Potassium channel subfamily K member 2 | protein | 273 | 77% helix, 0% strand | — |
Ligands and binding sites
- D12 · Dodecane · ligand · 3 copies · chains A
- R2R · ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2) · 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 · 3 copies · chains A, B
- HEX · Hexane · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.73 | 0.77 | 82 | R2R, CD |
| 2 | 522 | 0.64 | 0.76 | 41 | K |
| 3 | 107 | 0.57 | 0.85 | 22 | empty |
| 4 | 77 | 0.57 | 0.87 | 15 | empty |
| 5 | 147 | 0.46 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 4958 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 disulfide (additive adduct, disulfide).
Compared structures
- 6V3I · K2P2.1(TREK-1)I110D:RuR 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 6V3I · PDBe 6V3I
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