Research workbench
Crystal structure of the GLUR5 ligand binding core dimer in complex with UBP318 at 1.80 ångströms resolution
Analyse Crystal structure of the GLUR5 ligand binding core dimer in complex with UBP318… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QS2
- Type
- protein
- Length
- 502 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor, ionotropic kainate 1
- UniProt
- P22756
- Ligands
- UBF, CL
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutamate receptor, ionotropic kainate 1 | protein | 251 | 39% helix, 22% strand | P22756 |
Ligands and binding sites
- UBF · 3-({3-[(2S)-2-amino-2-carboxyethyl]-5-bromo-2,6-dioxo-3,6-dihydropyrimidin-1(2H)-yl}methyl)thiophene-2-carboxylic acid · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 754 | 0.75 | 0.80 | 60 | empty |
| 2 | 344 | 0.59 | 0.77 | 34 | UBF |
| 3 | 387 | 0.59 | 0.76 | 42 | UBF |
Interfaces
1 interface between chains.
- A–B · 651 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2QS2 · Crystal structure of the GluR5 ligand binding core dimer in complex with UBP318 at 1.80… · the same entry in another collection · chain A against A, TM-score 1.00
- P22756 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, kainate 1 (P22756) · a predicted model of the same protein · chain A against A, TM-score 0.88
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 P22756
- Elsewhere: RCSB PDB 2QS2 · PDBe 2QS2 · UniProt P22756
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