Research workbench
Crystal structure of the GLUK2EM lbd dimer assembly complex with glutamate and LY466195
Analyse Crystal structure of the GLUK2EM lbd dimer assembly complex with glutamate and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
- 5CMK · Crystal structure of the GluK2EM LBD dimer assembly complex with glutamate and LY466195 · the same entry in another collection · chain A against A, TM-score 1.00
- 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
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