Research workbench
X-ray structure of the GLUR2 ligand binding core (S1S2J-Y702F) in complex with acpa at 1.95 a resolution
Analyse X-ray structure of the GLUR2 ligand binding core (S1S2J-Y702F) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1M5F
- Type
- protein
- Length
- 774 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- AM1, ZN
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Glutamate receptor 2 | protein | 258 | 38% helix, 20% strand | P19491 |
Ligands and binding sites
- AM1 · (S)-2-amino-3-(3-carboxy-5-methylisoxazol-4-yl)propionic acid · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
- ACT · Acetate ion · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.74 | 0.99 | 21 | AM1 |
| 2 | 486 | 0.74 | 0.83 | 83 | empty |
| 3 | 771 | 0.73 | 0.79 | 75 | ACT, ZN |
| 4 | 54 | 0.71 | 0.98 | 20 | AM1 |
| 5 | 52 | 0.71 | 0.98 | 21 | AM1 |
Interfaces
3 interfaces between chains.
- A–C · 1117 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 303 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 82 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1M5F · X-ray structure of the GLUR2 ligand binding core (S1S2J-Y702F) in complex with acpa at… · the same entry in another collection · chain A against A, TM-score 1.00
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 1M5F · PDBe 1M5F · UniProt P19491
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