Research workbench
Crystal structure of the GLUA2O lbd in complex with glutamate and HBT1
Analyse Crystal structure of the GLUA2O lbd in complex with glutamate and HBT1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YBF
- Type
- protein
- Length
- 1,560 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2,GLUTAMATE receptor 2
- UniProt
- P42262
- Ligands
- GLU, 8SR, ZN
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Glutamate receptor 2,GLUTAMATE receptor 2 | protein | 260 | 38% helix, 21% strand | P42262 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 6 copies · chains A, B, C, D, E, F
- 8SR · 2-[2-[5-methyl-3-(trifluoromethyl)pyrazol-1-yl]ethanoylamino]-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide · ligand · 3 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 10 copies · chains A, C, B, D, E, F
- ACT · Acetate ion · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.83 | 0.84 | 134 | 8SR, ACT |
| 2 | 994 | 0.82 | 0.83 | 133 | ACT, 8SR |
| 3 | 561 | 0.80 | 0.86 | 98 | 8SR |
| 4 | 53 | 0.53 | 0.89 | 26 | empty |
| 5 | 68 | 0.52 | 0.87 | 25 | empty |
Interfaces
7 interfaces between chains.
- E–F · 1050 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1045 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1007 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 339 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 293 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5YBF · Crystal structure of the GluA2o LBD in complex with glutamate and HBT1 · the same entry in another collection · chain C against C, TM-score 1.00
- P42262 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P42262) · 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 P42262
- Elsewhere: RCSB PDB 5YBF · PDBe 5YBF · UniProt P42262
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