MolNFT v1 · #140457 · protein
Crystal structure of the GLUA2O lbd in complex with glutamate and HBT1
5YBF · Glutamate receptor 2,GLUTAMATE receptor 2: “Crystal structure of the GLUA2O lbd in complex with glutamate and HBT1”. X-ray diffraction, 3 ligands (GLU, 8SR, ZN), 12 pockets (best druggability 0.83). MolNFT v1 #140457 on GenesisL1…
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.