MolNFT v1 · #118255 · protein
Crystal structure of amino terminal domains of the NMDA receptor subunit GLUN1 and GLUN2B in complex with ifenprodil
5EWJ · NMDA glutamate receptor subunit: “Crystal structure of amino terminal domains of the NMDA receptor subunit GLUN1 and GLUN2B in complex with…”. X-ray diffraction, 5 ligands (QEL, NAG, MAN), 18 pockets (best druggability 0.76). MolNFT…
- PDB
- 5EWJ
- Type
- protein
- Length
- 1,421 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NMDA glutamate receptor subunit; Glutamate receptor ionotropic, NMDA 2B
- UniProt
- Q91977, Q13224
- Ligands
- QEL, NAG, MAN, BMA, NA
- Pockets
- 18 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NMDA glutamate receptor subunit | protein | 357 | 38% helix, 24% strand | Q91977 |
| B | Glutamate receptor ionotropic, NMDA 2B | protein | 353 | 32% helix, 24% strand | Q13224 |
| C | NMDA glutamate receptor subunit | protein | 356 | 38% helix, 25% strand | Q91977 |
| D | Glutamate receptor ionotropic, NMDA 2B | protein | 355 | 33% helix, 23% strand | Q13224 |
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
- 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
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 742 | 0.76 | 0.81 | 86 | QEL |
| 2 | 734 | 0.75 | 0.80 | 83 | QEL |
| 3 | 187 | 0.67 | 0.86 | 34 | empty |
| 4 | 106 | 0.66 | 0.90 | 26 | empty |
| 5 | 106 | 0.62 | 0.88 | 29 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1263 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1247 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 775 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 5EWJ · 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
- Q13224 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2B (Q13224) · a predicted model of the same protein · chain B 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 Q13224
- Elsewhere: RCSB PDB 5EWJ · PDBe 5EWJ · UniProt Q91977 · UniProt Q13224
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