MolNFT v1 · #115529 · protein
Crystal structure of the GLUK2EM lbd dimer assembly complex with glutamate and LY466195
5CMK · Glutamate receptor ionotropic, kainate 2: “Crystal structure of the GLUK2EM lbd dimer assembly complex with glutamate and LY466195”. X-ray diffraction, 5 ligands (GLU, LY5, LI), 3 pockets (best druggability 0.80). MolNFT v1 #115529…
- PDB
- 5CMK
- Type
- protein
- Length
- 504 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, kainate 2
- UniProt
- P42260
- Ligands
- GLU, LY5, LI, CL, SO4
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, kainate 2 | protein | 251 | 39% helix, 22% strand | P42260 |
| B | Glutamate receptor ionotropic, kainate 2 | protein | 253 | 39% helix, 24% strand | P42260 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · chains A
- LY5 · (3S,4aR,6S,8aR)-6-{[(2S)-2-carboxy-4,4-difluoropyrrolidin-1-yl]methyl}decahydroisoquinoline-3-carboxylic acid · ligand · chains B
- LI · Lithium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 929 | 0.80 | 0.82 | 103 | LY5 |
| 2 | 69 | 0.72 | 0.97 | 20 | GLU |
| 3 | 134 | 0.44 | 0.76 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1045 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- P42260 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, kainate 2 (P42260) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P42260
- Elsewhere: RCSB PDB 5CMK · PDBe 5CMK · UniProt P42260
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.