MolNFT v1 · #141687 · protein
Crystal structure of the GLUA2O lbd in complex with glutamate and compound-2
5ZG1 · Glutamate receptor 2: “Crystal structure of the GLUA2O lbd in complex with glutamate and compound-2”. X-ray diffraction, 3 ligands (GLU, 9C0, SO4), 4 pockets (best druggability 0.80). MolNFT v1 #141687 on GenesisL1: 3D structure…
- PDB
- 5ZG1
- Type
- protein
- Length
- 516 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P42262
- Ligands
- GLU, 9C0, SO4
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutamate receptor 2 | protein | 258 | 38% helix, 21% strand | P42262 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 2 copies · chains A, B
- 9C0 · 9-(4-~{tert}-butylphenyl)-3,4-dihydropyrido[2,1-C][1,2, 4]thiadiazine 2,2-dioxide · ligand · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 960 | 0.80 | 0.81 | 109 | 9C0, SO4, GOL |
| 2 | 198 | 0.65 | 0.85 | 24 | empty |
| 3 | 105 | 0.40 | 0.76 | 23 | empty |
| 4 | 75 | 0.36 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 932 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5ZG1 · Crystal structure of the GluA2o LBD in complex with glutamate and Compound-2 · the same entry in another collection · chain A against A, TM-score 1.00
- P42262 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P42262) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 5ZG1 · PDBe 5ZG1 · UniProt P42262
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