Research workbench
Crystal structure of amino terminal domains of the NMDA receptor subunit GLUN1 and GLUN2B in complex with ifenprodil
Analyse Crystal structure of amino terminal domains of the NMDA receptor subunit GLUN1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QEL
- Type
- protein
- Length
- 1,404 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NMDA glutamate receptor subunit; Glutamate [NMDA] receptor subunit epsilon-2
- UniProt
- Q91977, Q00960
- Ligands
- QEL, NAG, MAN, BMA, FUC, NA
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NMDA glutamate receptor subunit | protein | 355 | 37% helix, 25% strand | Q91977 |
| B | Glutamate [NMDA] receptor subunit epsilon-2 | protein | 353 | 32% helix, 24% strand | Q00960 |
| C | NMDA glutamate receptor subunit | protein | 351 | 37% helix, 25% strand | Q91977 |
| D | Glutamate [NMDA] receptor subunit epsilon-2 | protein | 345 | 31% helix, 23% strand | Q00960 |
Ligands and binding sites
- QEL · 4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol · ligand · 2 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar
- NA · Sodium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 695 | 0.75 | 0.81 | 81 | QEL |
| 2 | 672 | 0.75 | 0.81 | 81 | QEL |
| 3 | 301 | 0.72 | 0.85 | 52 | empty |
| 4 | 180 | 0.66 | 0.86 | 37 | empty |
| 5 | 167 | 0.61 | 0.84 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1227 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1135 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 663 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 3QEL · Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2B… · the same entry in another collection · chain A against A, TM-score 1.00
- Q00960 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2B (Q00960) · a predicted model of the same protein · chain D 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 Q91977
- Every structure of UniProt Q00960
- Elsewhere: RCSB PDB 3QEL · PDBe 3QEL · UniProt Q91977 · UniProt Q00960
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