Research workbench
AMPA subtype ionotropic glutamate receptor GLUA2 in complex with noncompetitive inhibitor GYKI53655
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
- 5L1H
- Type
- protein
- Length
- 3,095 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- GYK, NAG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Glutamate receptor 2 | protein | 773 | 40% helix, 18% strand | P19491 |
| D | Glutamate receptor 2 | protein | 776 | 39% helix, 18% strand | P19491 |
Ligands and binding sites
- GYK · (8R)-5-(4-aminophenyl)-N,8-dimethyl-8,9-dihydro-2H,7H-[1,3]dioxolo[4,5-h][2,3]benzodiazepine-7-carboxamide · 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 | 989 | 0.85 | 0.86 | 99 | empty |
| 2 | 524 | 0.85 | 0.91 | 43 | empty |
| 3 | 982 | 0.84 | 0.85 | 113 | empty |
| 4 | 898 | 0.76 | 0.79 | 96 | empty |
| 5 | 1162 | 0.76 | 0.78 | 108 | GYK |
Interfaces
6 interfaces between chains.
- A–B · 3660 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 3400 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 3071 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 2933 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 393 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 5 glycan (disulfide, N-glycosylation, glycation).
Compared structures
- 5L1H · 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 5L1H · PDBe 5L1H · UniProt P19491
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