Research workbench
X-ray structure of the ligand-binding core of GLUA2 in complex with (R)-5-hpca at 2.1 a resolution
Analyse X-ray structure of the ligand-binding core of GLUA2 in complex with (R)-5-hpca… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PD9
- Type
- protein
- Length
- 518 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- HA5, SO4, CL
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor 2 | protein | 258 | 38% helix, 22% strand | P19491 |
| B | Glutamate receptor 2 | protein | 260 | 39% helix, 21% strand | P19491 |
Ligands and binding sites
- HA5 · (5R)-3-hydroxy-4,5,6,7-tetrahydroisoxazolo[5,4-c]pyridine-5-carboxylic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 885 | 0.78 | 0.81 | 104 | CL, GOL |
| 2 | 54 | 0.71 | 0.98 | 17 | HA5 |
| 3 | 55 | 0.69 | 0.97 | 19 | HA5 |
| 4 | 283 | 0.60 | 0.79 | 34 | empty |
| 5 | 106 | 0.42 | 0.77 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 879 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3PD9 · X-ray structure of the ligand-binding core of GluA2 in complex with (R)-5-HPCA at 2.1 A… · 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 3PD9 · PDBe 3PD9 · UniProt P19491
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