MolNFT v1 · #74073 · protein
Crystal structure of the GLUK5 (KA2) atd crystallographic dimer at 1.4 ångström resolution
3OM0 · Glutamate receptor, ionotropic kainate 5: “Crystal structure of the GLUK5 (KA2) atd crystallographic dimer at 1.4 ångström resolution”. X-ray diffraction, 2 ligands (NAG, BMA), 5 pockets (best druggability 0.72). MolNFT v1 #74073 on…
- PDB
- 3OM0
- Type
- protein
- Length
- 369 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor, ionotropic kainate 5
- UniProt
- Q63273
- Ligands
- NAG, BMA
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor, ionotropic kainate 5 | protein | 369 | 37% helix, 20% strand | Q63273 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- BMA · beta-D-mannopyranose · sugar · chains A
- GOL · Glycerol · additive · 3 copies · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 619 | 0.72 | 0.80 | 76 | GOL |
| 2 | 85 | 0.36 | 0.76 | 16 | empty |
| 3 | 54 | 0.34 | 0.78 | 20 | empty |
| 4 | 59 | 0.34 | 0.77 | 11 | empty |
| 5 | 59 | 0.28 | 0.73 | 13 | empty |
Modifications
Observed in the structure: 5 glycan, 3 disulfide (N-glycosylation, disulfide).
Compared structures
- 3OM0 · Crystal structure of the GluK5 (KA2) ATD crystallographic dimer at 1.4 Angstrom resolution · the same entry in another collection · chain A against A, TM-score 1.00
- Q63273 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, kainate 5 (Q63273) · a predicted model of the same protein · chain A 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 Q63273
- Elsewhere: RCSB PDB 3OM0 · PDBe 3OM0 · UniProt Q63273
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