MolNFT v1 · #59610 · protein
Crystal structure of GLUR5 ligand-binding core in complex with sodium at 1.72 ångström resolution
3C32 · Glutamate receptor, ionotropic kainate 1: “Crystal structure of GLUR5 ligand-binding core in complex with sodium at 1.72 ångström resolution”. X-ray diffraction, 3 ligands (KAI, NA, CL), 4 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 3C32
- Type
- protein
- Length
- 508 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor, ionotropic kainate 1
- UniProt
- P22756
- Ligands
- KAI, NA, CL
- Pockets
- 4 · best druggability 0.78
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 | 254 | 39% helix, 22% strand | P22756 |
Ligands and binding sites
- KAI · 3-(carboxymethyl)-4-isopropenylproline · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 923 | 0.78 | 0.80 | 106 | GOL |
| 2 | 320 | 0.71 | 0.84 | 41 | KAI, GOL |
| 3 | 239 | 0.66 | 0.84 | 31 | KAI, GOL |
| 4 | 74 | 0.38 | 0.78 | 14 | GOL |
Interfaces
1 interface between chains.
- A–B · 1089 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3C32 · Crystal structure of GluR5 ligand-binding core in complex with sodium at 1.72 Angstrom… · 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 0.98
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 3C32 · PDBe 3C32 · UniProt P22756
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