MolNFT v1 · #59612 · protein
Crystal structure of GLUR5 ligand-binding core in complex with rubidium at 1.82 ångström resolution
3C34 · Glutamate receptor, ionotropic kainate 1: “Crystal structure of GLUR5 ligand-binding core in complex with rubidium at 1.82 ångström resolution”. X-ray diffraction, 3 ligands (KAI, RB, CL), 6 pockets (best druggability 0.73). MolNFT…
- PDB
- 3C34
- 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, RB, CL
- Pockets
- 6 · best druggability 0.73
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
- RB · Rubidium ion · metal · 6 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 655 | 0.73 | 0.80 | 74 | empty |
| 2 | 309 | 0.71 | 0.84 | 40 | KAI, GOL |
| 3 | 230 | 0.67 | 0.84 | 32 | KAI, GOL |
| 4 | 160 | 0.56 | 0.81 | 28 | empty |
| 5 | 147 | 0.54 | 0.81 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1090 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3C34 · Crystal structure of GluR5 ligand-binding core in complex with rubidium at 1.82 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 B 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 3C34 · PDBe 3C34 · UniProt P22756
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