MolNFT v1 · #121769 · protein
Glutamate- and glycine-bound GLUN1/GLUN2A agonist binding domains
5I57 · Glutamate receptor ionotropic, NMDA 1,GLUTAMATE receptor…: “Glutamate- and glycine-bound GLUN1/GLUN2A agonist binding domains”. X-ray diffraction, 2 ligands (GLY, GLU), 5 pockets (best druggability 0.80). MolNFT v1 #121769 on…
- PDB
- 5I57
- Type
- protein
- Length
- 558 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, NMDA 1,GLUTAMATE receptor ionotropic, NMDA 1; Glutamate…
- UniProt
- P35439, Q00959
- Ligands
- GLY, GLU
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, NMDA 1,GLUTAMATE receptor ionotropic, NMDA 1 | protein | 281 | 32% helix, 27% strand | P35439 |
| B | Glutamate receptor ionotropic, NMDA 2A,GLUTAMATE receptor ionotropic, NMDA 2A | protein | 277 | 35% helix, 26% strand | Q00959 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 916 | 0.80 | 0.82 | 103 | empty |
| 2 | 205 | 0.58 | 0.80 | 33 | GLU |
| 3 | 280 | 0.57 | 0.77 | 36 | empty |
| 4 | 71 | 0.57 | 0.89 | 25 | empty |
| 5 | 70 | 0.35 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1183 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5I57 · Glutamate- and glycine-bound GluN1/GluN2A agonist binding domains · the same entry in another collection · chain A against A, TM-score 1.00
- Q00959 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2A (Q00959) · a predicted model of the same protein · chain B against A, TM-score 0.98
- 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 0.96
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 Q00959
- Elsewhere: RCSB PDB 5I57 · PDBe 5I57 · UniProt P35439 · UniProt Q00959
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