Research workbench
Crystal structure of the GLUK2 (GLUR6) wild-type lbd dimer in complex with glutamate
Analyse Crystal structure of the GLUK2 (GLUR6) wild-type lbd dimer in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XXR
- Type
- protein
- Length
- 497 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, NA, CL
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor, ionotropic kainate 2 | protein | 248 | 40% helix, 22% strand | P42260 |
| B | Glutamate receptor, ionotropic kainate 2 | protein | 249 | 40% helix, 22% strand | P42260 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 846 | 0.78 | 0.81 | 109 | empty |
| 2 | 50 | 0.69 | 0.97 | 19 | GLU |
| 3 | 116 | 0.42 | 0.77 | 26 | empty |
| 4 | 94 | 0.40 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1068 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2XXR · Crystal structure of the GluK2 (GluR6) wild-type LBD dimer in complex with glutamate · 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 B against A, TM-score 0.97
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 2XXR · PDBe 2XXR · UniProt P42260
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