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Crystal structure of human GLUK2 ligand-binding core in complex with novel marine-derived toxins, neodysiherbaine a
Analyse Crystal structure of human GLUK2 ligand-binding core in complex with novel… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QXM
- Type
- protein
- Length
- 506 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, kainate 2
- UniProt
- Q13002
- Ligands
- NDZ
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, kainate 2 | protein | 250 | 40% helix, 22% strand | Q13002 |
| B | Glutamate receptor ionotropic, kainate 2 | protein | 256 | 39% helix, 21% strand | Q13002 |
Ligands and binding sites
- NDZ · (2R,3aR,6R,7R,7aR)-2-[(2S)-2-amino-2-carboxyethyl]-6,7-dihydroxyhexahydro-2H-furo[3,2-b]pyran-2-carboxylic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1148 | 0.81 | 0.83 | 94 | empty |
| 2 | 91 | 0.74 | 0.96 | 20 | NDZ |
| 3 | 122 | 0.70 | 0.91 | 29 | NDZ |
| 4 | 159 | 0.44 | 0.75 | 18 | empty |
| 5 | 81 | 0.41 | 0.79 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 667 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3QXM · Crystal Structure of Human GluK2 Ligand-Binding Core in Complex with Novel Marine-Derived… · the same entry in another collection · chain A against A, TM-score 1.00
- Q13002 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, kainate 2 (Q13002) · 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 Q13002
- Elsewhere: RCSB PDB 3QXM · PDBe 3QXM · UniProt Q13002
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