Research workbench
X-ray structure of the ligand-binding core of GLUA2 in complex with (S)-7-hpca at 2.5 a resolution
Analyse X-ray structure of the ligand-binding core of GLUA2 in complex with (S)-7-hpca… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PD8
- Type
- protein
- Length
- 780 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- HA7, ZN
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor 2 | protein | 259 | 38% helix, 21% strand | P19491 |
| B | Glutamate receptor 2 | protein | 261 | 38% helix, 21% strand | P19491 |
| C | Glutamate receptor 2 | protein | 260 | 36% helix, 21% strand | P19491 |
Ligands and binding sites
- HA7 · (7S)-3-hydroxy-4,5,6,7-tetrahydroisoxazolo[5,4-c]pyridine-7-carboxylic acid · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 5 copies · chains A, B, C
- GOL · Glycerol · additive · chains A, B
- ACY · Acetic acid · additive · chains A
- CAC · Cacodylate ion · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1007 | 0.83 | 0.84 | 123 | GOL |
| 2 | 53 | 0.71 | 0.99 | 18 | HA7 |
| 3 | 51 | 0.71 | 0.99 | 19 | HA7 |
| 4 | 52 | 0.70 | 0.98 | 17 | HA7 |
| 5 | 261 | 0.56 | 0.78 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 930 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 287 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 71 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3PD8 · X-ray structure of the ligand-binding core of GluA2 in complex with (S)-7-HPCA at 2.5 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 3PD8 · PDBe 3PD8 · UniProt P19491
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