MolNFT v1 · #54726 · protein
Crystal structure of the GLUK2 (GLUR6) D776K lbd dimer in complex with glutamate (P21 21 21)
2XXX · Glutamate receptor, ionotropic kainate 2: “Crystal structure of the GLUK2 (GLUR6) D776K lbd dimer in complex with glutamate (P21 21 21)”. X-ray diffraction, 1 ligand (GLU), 11 pockets (best druggability 0.80). MolNFT v1 #54726 on…
- PDB
- 2XXX
- Type
- protein
- Length
- 990 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor, ionotropic kainate 2
- UniProt
- P42260
- Ligands
- GLU
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Glutamate receptor, ionotropic kainate 2 | protein | 248 | 40% helix, 22% strand | P42260 |
| D | Glutamate receptor, ionotropic kainate 2 | protein | 246 | 39% helix, 22% strand | P42260 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1138 | 0.80 | 0.82 | 107 | empty |
| 2 | 1128 | 0.79 | 0.80 | 137 | empty |
| 3 | 70 | 0.62 | 0.91 | 18 | empty |
| 4 | 155 | 0.60 | 0.84 | 42 | GLU |
| 5 | 136 | 0.45 | 0.77 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1184 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1147 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 420 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 281 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 192 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2XXX · Crystal structure of the GluK2 (GluR6) D776K LBD dimer in complex with glutamate (P21 21… · the same entry in another collection · chain C against C, 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 C 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 2XXX · PDBe 2XXX · UniProt P42260
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