MolNFT v1 · #46944 · protein
Structure and mechanism of kainate receptor modulation by anions
2OJT · Glutamate receptor, ionotropic kainate 1: “Structure and mechanism of kainate receptor modulation by anions”. X-ray diffraction, 2 ligands (UBA, BR), 3 pockets (best druggability 0.72). MolNFT v1 #46944 on GenesisL1: 3D structure…
- PDB
- 2OJT
- Type
- protein
- Length
- 502 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor, ionotropic kainate 1
- UniProt
- P22756
- Ligands
- UBA, BR
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutamate receptor, ionotropic kainate 1 | protein | 251 | 39% helix, 22% strand | P22756 |
Ligands and binding sites
- UBA · (S)-1-(2-amino-2-carboxyethyl)-3(2-carboxythiophene-3-yl-methyl)-5-methylpyrimidine-2,4-dione · ligand · 2 copies · chains A, B
- BR · Bromide ion · ion · 2 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 723 | 0.72 | 0.79 | 60 | empty |
| 2 | 327 | 0.59 | 0.77 | 37 | UBA |
| 3 | 362 | 0.57 | 0.75 | 40 | UBA |
Interfaces
1 interface between chains.
- A–B · 648 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2OJT · Structure and mechanism of kainate receptor modulation by anions · the same entry in another collection · chain A against A, TM-score 1.00
- P22756 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, kainate 1 (P22756) · a predicted model of the same protein · chain B against A, TM-score 0.89
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 P22756
- Elsewhere: RCSB PDB 2OJT · PDBe 2OJT · UniProt P22756
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