Research workbench
Crystal structure of the GLUR2 ligand binding core (S1S2J) T686S mutant in complex with glutamate at 1.7 resolution
Analyse Crystal structure of the GLUR2 ligand binding core (S1S2J) T686S mutant in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B6W
- Type
- protein
- Length
- 1,032 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- GLU, SO4
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glutamate receptor 2 | protein | 258 | 38% helix, 21% strand | P19491 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.81 | 0.83 | 113 | SO4 |
| 2 | 915 | 0.78 | 0.81 | 119 | SO4 |
| 3 | 612 | 0.64 | 0.75 | 69 | empty |
| 4 | 80 | 0.63 | 0.90 | 28 | empty |
| 5 | 280 | 0.59 | 0.79 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–C · 990 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 848 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 475 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3B6W · Crystal Structure of the GLUR2 Ligand Binding Core (S1S2J) T686S Mutant in Complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- P19491 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P19491) · a predicted model of the same protein · chain D 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 3B6W · PDBe 3B6W · UniProt P19491
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