Research workbench
Crystal structure of GLUN1/GLUN2A ligand-binding domain in complex with glycine and ppda
Analyse Crystal structure of GLUN1/GLUN2A ligand-binding domain in complex with glycine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NF6
- Type
- protein
- Length
- 556 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
- Ligands
- GLY, 2JL
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, NMDA 1 | protein | 278 | 32% helix, 29% strand | P35439 |
| B | Glutamate receptor ionotropic, NMDA 2A | protein | 278 | 33% helix, 27% strand | Q00959 |
Ligands and binding sites
- GLY · Glycine · ligand · chains A
- 2JL · (2S,3R)-1-(phenanthren-2-ylcarbonyl)piperazine-2,3-dicarboxylic acid · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 644 | 0.78 | 0.83 | 87 | empty |
| 2 | 485 | 0.71 | 0.81 | 55 | 2JL |
| 3 | 125 | 0.63 | 0.87 | 30 | empty |
| 4 | 120 | 0.46 | 0.78 | 27 | empty |
| 5 | 53 | 0.30 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1338 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4NF6 · Crystal structure of GluN1/GluN2A ligand-binding domain in complex with glycine and PPDA · 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 0.91
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 4NF6 · PDBe 4NF6 · UniProt P35439 · UniProt Q00959
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