Research workbench
X-ray structure of the GLUR2 ligand-binding core (S1S2J) in complex with (S)-des-me-AMPA at 1.46 a resolution. crystallization in the presence of lithium sulfate.
Analyse X-ray structure of the GLUR2 ligand-binding core (S1S2J) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MQD
- Type
- protein
- Length
- 1,032 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor subunit 2
- UniProt
- P19491
- Ligands
- SHI, SO4
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glutamate receptor subunit 2 | protein | 258 | 38% helix, 21% strand | P19491 |
Ligands and binding sites
- SHI · (S)-2-amino-3-(3-hydroxy-isoxazol-4-yl)propionic acid · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, D
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.69 | 0.98 | 18 | SHI |
| 2 | 689 | 0.66 | 0.75 | 72 | empty |
| 3 | 271 | 0.51 | 0.75 | 42 | empty |
| 4 | 116 | 0.43 | 0.77 | 21 | empty |
| 5 | 130 | 0.37 | 0.73 | 24 | empty |
Interfaces
2 interfaces between chains.
- B–C · 353 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 105 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1MQD · X-ray structure of the GluR2 ligand-binding core (S1S2J) in complex with (S)-Des-Me-AMPA… · the same entry in another collection · chain A against A, TM-score 1.00
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 P19491
- Elsewhere: RCSB PDB 1MQD · PDBe 1MQD · UniProt P19491
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