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Structure of GluA2o ligand-binding domain (S1S2J) in complex with glutamate and sodium bromide at 1.95 A resolution
Analyse Structure of GluA2o ligand-binding domain (S1S2J) in complex with glutamate and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GL4
- Type
- protein
- Length
- 526 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.948
- Source
- Rattus norvegicus
- Molecule
- Glutamate receptor 2,Glutamate receptor 2
- UniProt
- P19491
- Ligands
- GLU, NA, BR
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · resolution 1.948 · 1 distinct chain · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutamate receptor 2,Glutamate receptor 2 | protein | 263 | 38% helix, 21% strand | P19491 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains B
- BR · Bromide ion · ion · 6 copies · chains A, B
- GOL · Glycerol · additive · chains A
- ACT · Acetate ion · additive · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 859 | 0.72 | 0.77 | 68 | BR |
| 2 | 115 | 0.43 | 0.77 | 25 | empty |
| 3 | 81 | 0.37 | 0.77 | 23 | empty |
| 4 | 54 | 0.37 | 0.80 | 17 | BR |
Interfaces
1 interface between chains.
- A–B · 348 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6GL4 · Structure of GLUA2O ligand-binding domain (S1S2J) in complex with glutamate and sodium… · the same entry in another collection · chain A against A, TM-score 1.00
- P19491 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P19491) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 6GL4 · PDBe 6GL4 · UniProt P19491
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