MolNFT v1 · #128505 · protein
Crystal structure of the GLUA2 lbd (L483Y-N754S-L758V) in complex with glutamate
5NS9 · Glutamate receptor 2,GLUTAMATE receptor 2: “Crystal structure of the GLUA2 lbd (L483Y-N754S-L758V) in complex with glutamate”. X-ray diffraction, 3 ligands (GLU, NA, SO4), 4 pockets (best druggability 0.77). MolNFT v1 #128505 on…
- PDB
- 5NS9
- Type
- protein
- Length
- 524 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2,GLUTAMATE receptor 2
- UniProt
- P19491
- Ligands
- GLU, NA, SO4
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor 2,GLUTAMATE receptor 2 | protein | 263 | 38% helix, 21% strand | P19491 |
| B | Glutamate receptor 2,GLUTAMATE receptor 2 | protein | 261 | 38% helix, 21% strand | P19491 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 5 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · chains A
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 | 835 | 0.77 | 0.81 | 108 | SO4, NA |
| 2 | 291 | 0.59 | 0.79 | 34 | NA |
| 3 | 109 | 0.41 | 0.76 | 25 | empty |
| 4 | 75 | 0.37 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1038 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5NS9 · Crystal structure of the GluA2 LBD (L483Y-N754S-L758V) in complex with glutamate · the same entry in another collection · chain A against A, TM-score 1.00
- P19491 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P19491) · a predicted model of the same protein · chain A 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 P19491
- Elsewhere: RCSB PDB 5NS9 · PDBe 5NS9 · UniProt P19491
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