Research workbench
Crystal structure of the GLUR5 ligand binding core dimer with glutamate at 2.1 ångströms resolution
Analyse Crystal structure of the GLUR5 ligand binding core dimer with glutamate at 2.1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F36
- Type
- protein
- Length
- 1,004 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor, ionotropic kainate 1
- UniProt
- P22756
- Ligands
- GLU, SO4
- Pockets
- 13 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate receptor, ionotropic kainate 1 | protein | 254 | 39% helix, 21% strand | P22756 |
| B, D | Glutamate receptor, ionotropic kainate 1 | protein | 248 | 40% helix, 22% strand | P22756 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 656 | 0.86 | 0.91 | 82 | SO4 |
| 2 | 539 | 0.86 | 0.91 | 65 | SO4 |
| 3 | 494 | 0.76 | 0.84 | 59 | empty |
| 4 | 632 | 0.73 | 0.80 | 60 | empty |
| 5 | 65 | 0.73 | 0.98 | 20 | GLU |
Interfaces
5 interfaces between chains.
- A–B · 1225 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1149 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 879 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 746 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 596 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2F36 · Crystal Structure of the GluR5 Ligand Binding Core Dimer with Glutamate At 2.1 Angstroms… · the same entry in another collection · chain C against C, 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 D 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 P22756
- Elsewhere: RCSB PDB 2F36 · PDBe 2F36 · UniProt P22756
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.