Research workbench
Crystal structure of GLUN2D ligand-binding core in complex with N- methyl-D-aspartate
Analyse Crystal structure of GLUN2D ligand-binding core in complex with N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OEM
- Type
- protein
- Length
- 268 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate [NMDA] receptor subunit epsilon-4
- UniProt
- Q62645
- Ligands
- OEM
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate [NMDA] receptor subunit epsilon-4 | protein | 268 | 34% helix, 24% strand | Q62645 |
Ligands and binding sites
- OEM · N-methyl-D-aspartic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.59 | 0.81 | 37 | OEM |
| 2 | 58 | 0.35 | 0.79 | 17 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3OEM · Crystal structure of GluN2D ligand-binding core in complex with N-methyl-D-aspartate · 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 0.95
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 3OEM · PDBe 3OEM · UniProt Q62645
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