Research workbench
Crystal structure of the GLUR6 amino terminal domain dimer assembly mpd form
Analyse Crystal structure of the GLUR6 amino terminal domain dimer assembly mpd form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H6H
- Type
- protein
- Length
- 762 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor, ionotropic kainate 2
- UniProt
- P42260
- Ligands
- NAG, CA
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor, ionotropic kainate 2 | protein | 383 | 34% helix, 22% strand | P42260 |
| B | Glutamate receptor, ionotropic kainate 2 | protein | 379 | 35% helix, 22% strand | P42260 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1173 | 0.81 | 0.82 | 117 | empty |
| 2 | 220 | 0.58 | 0.80 | 25 | empty |
| 3 | 198 | 0.51 | 0.77 | 36 | empty |
| 4 | 182 | 0.49 | 0.77 | 26 | empty |
| 5 | 113 | 0.47 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1729 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 3H6H · Crystal structure of the GluR6 amino terminal domain dimer assembly MPD form · 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 P42260
- Elsewhere: RCSB PDB 3H6H · PDBe 3H6H · UniProt P42260
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