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Crystal structure of the GLUA2 ligand-binding domain (S1S2J) in complex with the agonist cbg-IV at 2.05A resolution
Analyse Crystal structure of the GLUA2 ligand-binding domain (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
- 4G8M
- Type
- protein
- Length
- 523 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- G8M, SO4, CL
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor 2 | protein | 260 | 37% helix, 22% strand | P19491 |
| B | Glutamate receptor 2 | protein | 263 | 38% helix, 21% strand | P19491 |
Ligands and binding sites
- G8M · (1S,2R)-2-[(S)-amino(carboxy)methyl]cyclobutanecarboxylic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 619 | 0.75 | 0.81 | 75 | GOL, CL |
| 2 | 62 | 0.71 | 0.97 | 20 | G8M |
| 3 | 61 | 0.70 | 0.96 | 19 | G8M |
| 4 | 219 | 0.62 | 0.82 | 31 | empty |
| 5 | 289 | 0.60 | 0.79 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 935 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4G8M · Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with the agonist… · 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 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 P19491
- Elsewhere: RCSB PDB 4G8M · PDBe 4G8M · UniProt P19491
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