MolNFT v1 · #74074 · protein
Crystal structure of the GLUK5 (KA2) atd dimer at 1.7 ångström resolution
3OM1 · Glutamate receptor ionotropic, kainate 5: “Crystal structure of the GLUK5 (KA2) atd dimer at 1.7 ångström resolution”. X-ray diffraction, 2 ligands (NAG, NA), 8 pockets (best druggability 0.80). MolNFT v1 #74074 on GenesisL1: 3D…
- 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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