Research workbench
Crystal structure of the GLUK5 (KA2) atd dimer at 1.7 ångström resolution
Analyse Crystal structure of the GLUK5 (KA2) atd dimer at 1.7 ångström resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OM1
- Type
- protein
- Length
- 740 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, kainate 5
- UniProt
- Q63273
- Ligands
- NAG, NA
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, kainate 5 | protein | 373 | 39% helix, 20% strand | Q63273 |
| B | Glutamate receptor ionotropic, kainate 5 | protein | 367 | 39% helix, 20% strand | Q63273 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.80 | 0.81 | 109 | empty |
| 2 | 491 | 0.72 | 0.81 | 62 | NAG |
| 3 | 76 | 0.62 | 0.90 | 17 | empty |
| 4 | 124 | 0.55 | 0.82 | 30 | empty |
| 5 | 165 | 0.53 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1287 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 3OM1 · Crystal structure of the GluK5 (KA2) ATD dimer at 1.7 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 B 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 Q63273
- Elsewhere: RCSB PDB 3OM1 · PDBe 3OM1 · UniProt Q63273
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