MolNFT v1 · #21519 · protein
Crystal structure of the GLUR6 ligand binding core in complex with 2S, 4R-4-methylglutamate at 1.8 ångström resolution
1SD3 · Glutamate receptor, ionotropic kainate 2: “Crystal structure of the GLUR6 ligand binding core in complex with 2S, 4R-4-methylglutamate at 1.8 ångström…”. X-ray diffraction, 1 ligand (SYM), 7 pockets (best druggability 0.81). MolNFT…
- PDB
- 1SD3
- Type
- protein
- Length
- 502 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor, ionotropic kainate 2
- UniProt
- P42260
- Ligands
- SYM
- Pockets
- 7 · best druggability 0.81
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 2 | protein | 251 | 39% helix, 22% strand | P42260 |
Ligands and binding sites
- SYM · 2S,4R-4-methylglutamate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1004 | 0.81 | 0.82 | 81 | empty |
| 2 | 53 | 0.68 | 0.97 | 21 | SYM |
| 3 | 206 | 0.51 | 0.76 | 30 | empty |
| 4 | 103 | 0.42 | 0.77 | 23 | empty |
| 5 | 115 | 0.40 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 645 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1SD3 · Crystal structure of the GLUR6 ligand binding core in complex with… · the same entry in another collection · chain B against B, 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 0.96
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 P42260
- Elsewhere: RCSB PDB 1SD3 · PDBe 1SD3 · UniProt P42260
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