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Crystal structure of GLUN1/GLUN2A NMDA receptor agonist binding domains with glycine and antagonist, 4-(3-FLUOROPROPYL)PHENYL-acepc
Analyse Crystal structure of GLUN1/GLUN2A NMDA receptor agonist binding domains with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VII
- Type
- protein
- Length
- 546 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 2A
- UniProt
- P35439, Q00959, G3V9C5
- Ligands
- GLY, 5DY
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, NMDA 1 | protein | 269 | 33% helix, 27% strand | P35439 |
| B | Glutamate receptor ionotropic, NMDA 2A | protein | 277 | 36% helix, 26% strand | Q00959, G3V9C5 |
Ligands and binding sites
- GLY · Glycine · ligand · chains A
- 5DY · 5-[(2R)-2-amino-2-carboxyethyl]-1-[4-(3-fluoropropyl) phenyl]-1H-pyrazole-3-carboxylic acid · ligand · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 823 | 0.80 | 0.83 | 112 | empty |
| 2 | 429 | 0.72 | 0.82 | 51 | 5DY, PEG, TRS |
| 3 | 101 | 0.45 | 0.79 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1287 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 covalent (disulfide, additive adduct).
Compared structures
- 5VII · Crystal structure of GluN1/GluN2A NMDA receptor agonist binding domains with glycine and… · the same entry in another collection · chain B against B, TM-score 1.00
- 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 0.97
- 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 0.95
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
- Every structure of UniProt G3V9C5
- Elsewhere: RCSB PDB 5VII · PDBe 5VII · UniProt P35439 · UniProt Q00959 · UniProt G3V9C5
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