MolNFT v1 · #103353 · protein
Crystal structure of GLUN1A/GLUN2B NMDA receptor ion channel
4PE5 · Glutamate receptor ionotropic, NMDA 1: “Crystal structure of GLUN1A/GLUN2B NMDA receptor ion channel”. X-ray diffraction, 7 ligands (GLY, QEL, GLU), 20 pockets (best druggability 0.80). MolNFT v1 #103353 on GenesisL1: 3D structure…
- PDB
- 4PE5
- Type
- protein
- Length
- 2,944 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, NMDA 1; Glutamate receptor ionotropic, NMDA 2B
- UniProt
- P35439, Q00960
- Ligands
- GLY, QEL, GLU, NAG, MAN, BMA, W
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, NMDA 1 | protein | 743 | 38% helix, 21% strand | P35439 |
| B | Glutamate receptor ionotropic, NMDA 2B | protein | 720 | 36% helix, 20% strand | Q00960 |
| C | Glutamate receptor ionotropic, NMDA 1 | protein | 754 | 37% helix, 20% strand | P35439 |
| D | Glutamate receptor ionotropic, NMDA 2B | protein | 727 | 35% helix, 20% strand | Q00960 |
Ligands and binding sites
- GLY · Glycine · ligand · 2 copies · chains A, C
- QEL · 4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol · ligand · 2 copies · chains A, B, C, D
- GLU · Glutamic acid · ligand · 2 copies · chains B, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 9 copies
- BMA · beta-D-mannopyranose · sugar · 5 copies
- W · Tungsten ion · metal · 84 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1020 | 0.80 | 0.81 | 103 | empty |
| 2 | 1091 | 0.78 | 0.80 | 107 | empty |
| 3 | 973 | 0.78 | 0.80 | 131 | empty |
| 4 | 856 | 0.77 | 0.81 | 102 | empty |
| 5 | 1005 | 0.75 | 0.77 | 85 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2048 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1764 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1485 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 1241 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 178 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 14 glycan (disulfide, N-glycosylation).
Compared structures
- 4PE5 · Crystal Structure of GluN1a/GluN2B NMDA Receptor Ion Channel · the same entry in another collection · chain C against C, 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 B against A, TM-score 0.90
- P35439 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 1 (P35439) · a predicted model of the same protein · chain A against A, TM-score 0.87
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 P35439
- Every structure of UniProt Q00960
- Elsewhere: RCSB PDB 4PE5 · PDBe 4PE5 · UniProt P35439 · UniProt Q00960
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