Research workbench
Crystal structure of the binding domain of the AMPA subunit GLUR2 bound to glutamate
Analyse Crystal structure of the binding domain of the AMPA subunit GLUR2 bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DP6
- Type
- protein
- Length
- 774 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- GLU, ZN
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Glutamate receptor 2 | protein | 258 | 39% helix, 21% strand | P19491 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 6 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.79 | 0.86 | 85 | empty |
| 2 | 507 | 0.70 | 0.80 | 51 | empty |
| 3 | 271 | 0.58 | 0.78 | 32 | empty |
| 4 | 99 | 0.38 | 0.75 | 22 | empty |
| 5 | 72 | 0.37 | 0.77 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1007 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 284 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 55 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3DP6 · Crystal structure of the binding domain of the AMPA subunit GluR2 bound to glutamate · the same entry in another collection · chain B against B, 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 0.98
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 3DP6 · PDBe 3DP6 · UniProt P19491
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