Research workbench
Electron density MAP of GLUK2 desensitized state in complex with 2S, 4R-4-methylglutamate
Analyse Electron density MAP of GLUK2 desensitized state in complex with 2S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UQQ
- Type
- protein
- Length
- 2,762 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, kainate 2
- UniProt
- P42260
- Ligands
- GLU
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 2 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate receptor ionotropic, kainate 2 | protein | 693 | 40% helix, 21% strand | P42260 |
| B, D | Glutamate receptor ionotropic, kainate 2 | protein | 688 | 40% helix, 21% strand | P42260 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1047 | 0.82 | 0.83 | 105 | empty |
| 2 | 986 | 0.82 | 0.83 | 90 | empty |
| 3 | 888 | 0.71 | 0.76 | 104 | empty |
| 4 | 52 | 0.70 | 0.98 | 18 | GLU |
| 5 | 51 | 0.68 | 0.97 | 19 | GLU |
Interfaces
6 interfaces between chains.
- C–D · 2504 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 2498 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1015 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 1013 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 186 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4UQQ · Electron density map of GluK2 desensitized state in complex with 2S,4R-4-methylglutamate · the same entry in another collection · chain C against C, TM-score 1.00
- P42260 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, kainate 2 (P42260) · a predicted model of the same protein · chain C against A, TM-score 0.88
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 P42260
- Elsewhere: RCSB PDB 4UQQ · PDBe 4UQQ · UniProt P42260
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