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Crystal structure of amino terminal domains of the NMDA receptor subunit GLUN1 and GLUN2B in complex with ro 25-6981
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
- 3QEM
- Type
- protein
- Length
- 1,408 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
- QEM, NAG, MAN, BMA, NA
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NMDA glutamate receptor subunit | protein | 355 | 36% helix, 25% strand | Q91977 |
| B | Glutamate [NMDA] receptor subunit epsilon-2 | protein | 356 | 32% helix, 23% strand | Q00960 |
| C | NMDA glutamate receptor subunit | protein | 352 | 37% helix, 23% strand | Q91977 |
| D | Glutamate [NMDA] receptor subunit epsilon-2 | protein | 345 | 31% helix, 21% strand | Q00960 |
Ligands and binding sites
- QEM · 4-[(1R,2S)-3-(4-benzylpiperidin-1-yl)-1-hydroxy-2-methylpropyl]phenol · ligand · 2 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · 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
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 690 | 0.76 | 0.81 | 81 | QEM |
| 2 | 418 | 0.76 | 0.85 | 74 | empty |
| 3 | 720 | 0.76 | 0.81 | 77 | QEM |
| 4 | 215 | 0.67 | 0.85 | 47 | empty |
| 5 | 164 | 0.64 | 0.85 | 36 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1230 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 965 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 635 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 3QEM · 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 3QEM · PDBe 3QEM · UniProt Q91977 · UniProt Q00960
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