MolNFT v2 · #227856 · protein
Ligand-binding and transmembrane domains of kainate receptor GluK2 in complex with positive allosteric modulator BPAM-344 and channel blocker Spermine
9DXS · Glutamate receptor ionotropic, kainate 2: “Ligand-binding and transmembrane domains of kainate receptor GluK2 in complex with positive allosteric…”. Electron microscopy at 3.55, 6 ligands (POV, CLR, 2J9), 19 pockets (best…
- PDB
- 9DXS
- Type
- protein
- Length
- 1,784 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.55
- Source
- Rattus norvegicus
- Molecule
- Glutamate receptor ionotropic, kainate 2
- UniProt
- P42260
- Ligands
- POV, CLR, 2J9, SPM, NAG, BMA
- Pockets
- 19 · best druggability 0.85
Structure
electron microscopy · resolution 3.55 · 1 distinct chain · 44% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glutamate receptor ionotropic, kainate 2 | protein | 446 | 44% helix, 8% strand | P42260 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 12 copies · chains A, D, B, C
- CLR · Cholesterol · ligand · 8 copies · chains A, D, B, C
- 2J9 · 4-cyclopropyl-7-fluoro-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide · ligand · 4 copies · chains A, D, B, C
- SPM · Spermine · ligand · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.85 | 0.86 | 123 | 2J9 |
| 2 | 1103 | 0.84 | 0.84 | 109 | 2J9 |
| 3 | 494 | 0.82 | 0.89 | 52 | SPM |
| 4 | 424 | 0.66 | 0.79 | 45 | empty |
| 5 | 509 | 0.65 | 0.77 | 51 | empty |
Interfaces
6 interfaces between chains.
- A–D · 3973 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 3908 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2701 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2656 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 122 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- P42260 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, kainate 2 (P42260) · a predicted model of the same protein · chain B against A, TM-score 0.67
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 9DXS · PDBe 9DXS · UniProt P42260
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