Research workbench
Full-length AMPA subtype ionotropic glutamate receptor GLUA2 in complex with partial agonist kainate
Analyse Full-length AMPA subtype ionotropic glutamate receptor GLUA2 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
- 4U2Q
- Type
- protein
- Length
- 2,960 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- KAI, NAG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor 2 | protein | 721 | 40% helix, 19% strand | P19491 |
| B | Glutamate receptor 2 | protein | 746 | 40% helix, 19% strand | P19491 |
| C | Glutamate receptor 2 | protein | 744 | 40% helix, 18% strand | P19491 |
| D | Glutamate receptor 2 | protein | 749 | 40% helix, 18% strand | P19491 |
Ligands and binding sites
- KAI · 3-(carboxymethyl)-4-isopropenylproline · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.85 | 0.86 | 118 | KAI |
| 2 | 1004 | 0.84 | 0.84 | 98 | empty |
| 3 | 790 | 0.81 | 0.84 | 115 | KAI |
| 4 | 911 | 0.81 | 0.83 | 77 | empty |
| 5 | 952 | 0.81 | 0.83 | 84 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2819 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2622 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 2197 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 2184 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 426 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4U2Q · Full-length AMPA subtype ionotropic glutamate receptor GluA2 in complex with partial… · 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 C against A, TM-score 0.86
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 4U2Q · PDBe 4U2Q · UniProt P19491
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