Research workbench
Crystal structure of GluN2D ligand-binding core in complex with L-glutamate
Analyse Crystal structure of GluN2D ligand-binding core in complex with L-glutamate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OEN
- Type
- protein
- Length
- 250 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Rattus norvegicus
- Molecule
- Glutamate [NMDA] receptor subunit epsilon-4
- UniProt
- Q62645
- Ligands
- GLU
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · resolution 1.8 · 1 distinct chain · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate [NMDA] receptor subunit epsilon-4 | protein | 250 | 38% helix, 26% strand | Q62645 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.60 | 0.79 | 44 | GLU |
| 2 | 53 | 0.35 | 0.79 | 19 | empty |
| 3 | 52 | 0.31 | 0.75 | 13 | empty |
| 4 | 71 | 0.31 | 0.74 | 15 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3OEN · Crystal structure of GLUN2D ligand-binding core in complex with L- glutamate · the same entry in another collection · chain A against A, TM-score 1.00
- Q62645 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2D (Q62645) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q62645
- Elsewhere: RCSB PDB 3OEN · PDBe 3OEN · UniProt Q62645
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