MolNFT v1 · #114611 · protein
Crystal structure of the GLUA2 ligand-binding domain (L483Y-N754S) in complex with glutamate and bpam-321 at 2.07 a resolution
5BUU · Glutamate receptor 2,GLUTAMATE receptor 2: “Crystal structure of the GLUA2 ligand-binding domain (L483Y-N754S) in complex with glutamate and bpam-321 at…”. X-ray diffraction, 3 ligands (4V6, GLU, SO4), 4 pockets (best druggability…
- PDB
- 5BUU
- Type
- protein
- Length
- 514 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
- 4V6, GLU, SO4
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor 2,GLUTAMATE receptor 2 | protein | 260 | 37% helix, 20% strand | P19491 |
| B | Glutamate receptor 2,GLUTAMATE receptor 2 | protein | 254 | 37% helix, 23% strand | P19491 |
Ligands and binding sites
- 4V6 · (3R)-7-chloro-2,3,4-trimethyl-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide · ligand · 2 copies · chains A, B
- GLU · Glutamic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 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 | 841 | 0.79 | 0.82 | 102 | 4V6, SO4, EDO |
| 2 | 283 | 0.61 | 0.80 | 35 | EDO |
| 3 | 81 | 0.36 | 0.76 | 24 | empty |
| 4 | 73 | 0.36 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 936 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5BUU · Crystal structure of the GluA2 ligand-binding domain (L483Y-N754S) in complex with… · 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 0.98
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 P19491
- Elsewhere: RCSB PDB 5BUU · PDBe 5BUU · UniProt P19491
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