Research workbench
AMPA subtype ionotropic glutamate receptor GLUA2 in complex with noncompetitive inhibitor CP465022
Analyse AMPA subtype ionotropic glutamate receptor GLUA2 in complex with noncompetitive… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L1E
- Type
- protein
- Length
- 3,100 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- 6ZQ, NAG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Glutamate receptor 2 | protein | 777 | 41% helix, 17% strand | P19491 |
| B, C | Glutamate receptor 2 | protein | 773 | 38% helix, 18% strand | P19491 |
Ligands and binding sites
- 6ZQ · 3-(2-chlorophenyl)-2-(2-{6-[(diethylamino) methyl]pyridin-2-yl}ethyl)-6-fluoroquinazolin-4(3H)-one · ligand · 4 copies · chains A, D, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.84 | 0.85 | 88 | empty |
| 2 | 976 | 0.83 | 0.85 | 118 | empty |
| 3 | 1087 | 0.81 | 0.83 | 106 | empty |
| 4 | 546 | 0.78 | 0.85 | 76 | empty |
| 5 | 1117 | 0.76 | 0.78 | 102 | 6ZQ |
Interfaces
6 interfaces between chains.
- A–B · 3847 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 3552 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 2976 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 2958 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 407 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 5L1E · AMPA subtype ionotropic glutamate receptor GluA2 in complex with noncompetitive inhibitor… · 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 5L1E · PDBe 5L1E · UniProt P19491
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