Research workbench
Crystal structure of an OPEN/CLOSED GLUA2 ligand-binding domain dimer at 1.91 a resolution
Analyse Crystal structure of an OPEN/CLOSED GLUA2 ligand-binding domain dimer at 1.91 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O3B
- Type
- protein
- Length
- 518 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- GLU, SO4, CL
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor 2 | protein | 260 | 38% helix, 21% strand | P19491 |
| B | Glutamate receptor 2 | protein | 258 | 38% helix, 21% strand | P19491 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · chains B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 6 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
- ACT · Acetate ion · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains 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 | 1050 | 0.78 | 0.80 | 111 | SO4, GOL, PEG, ACT |
| 2 | 296 | 0.59 | 0.78 | 32 | empty |
| 3 | 89 | 0.39 | 0.77 | 19 | SO4 |
| 4 | 97 | 0.37 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 944 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4O3B · Crystal structure of an open/closed glua2 ligand-binding domain dimer at 1.91 A resolution · the same entry in another collection · chain B against B, TM-score 1.00
- P19491 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P19491) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 4O3B · PDBe 4O3B · UniProt P19491
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