Research workbench
Crystal structure of the GLUA2 ligand-binding domain (S1S2J) in complex with (S)-2-amino-3-(5-(2-(3-chlorobenzyl)-2H-tetrazol-5-yl)- 3-hydroxyisoxazol-4-YL)PROPANOIC acid at 2.3 a 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
- 5FHO
- Type
- protein
- Length
- 1,024 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2,GLUTAMATE receptor 2
- UniProt
- P19491
- Ligands
- 5XN, SO4, CL
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor 2,GLUTAMATE receptor 2 | protein | 254 | 37% helix, 21% strand | P19491 |
| B | Glutamate receptor 2,GLUTAMATE receptor 2 | protein | 255 | 37% helix, 21% strand | P19491 |
| C | Glutamate receptor 2,GLUTAMATE receptor 2 | protein | 259 | 37% helix, 20% strand | P19491 |
| D | Glutamate receptor 2,GLUTAMATE receptor 2 | protein | 256 | 38% helix, 21% strand | P19491 |
Ligands and binding sites
- 5XN · (1S)-1-carboxy-2-(5-{2-[(3-chlorophenyl)methyl]-2H-tetrazol-5-yl}-3-oxo-2,3-dihydro-1,2-oxazol-4-yl)ethan-1-aminium · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, D, C
- CL · Chloride ion · ion · 9 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, D, B, C
- GOL · Glycerol · additive · 6 copies · chains A, D, B, C
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 888 | 0.76 | 0.79 | 89 | GOL, CL, EDO |
| 2 | 586 | 0.75 | 0.82 | 70 | CL, EDO |
| 3 | 102 | 0.74 | 0.95 | 24 | 5XN |
| 4 | 138 | 0.70 | 0.90 | 30 | 5XN |
| 5 | 132 | 0.70 | 0.90 | 30 | 5XN |
Interfaces
4 interfaces between chains.
- A–D · 1119 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 997 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 92 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 61 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5FHO · Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with… · 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 5FHO · PDBe 5FHO · UniProt P19491
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