Research workbench
Crystal structure of GLUN1/GLUN2A ligand-binding domain in complex with glycine and UBP791
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
- 6UZW
- Type
- protein
- Length
- 555 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, QM4
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, NMDA 1 | protein | 276 | 32% helix, 26% strand | P35439 |
| B | Glutamate receptor ionotropic, NMDA 2A | protein | 279 | 34% helix, 26% strand | Q00959 |
Ligands and binding sites
- GLY · Glycine · ligand · chains A
- QM4 · (2S,3R)-1-[7-(2-carboxyethyl)phenanthrene-2-carbonyl]piperazine-2,3-dicarboxylic acid · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.76 | 0.82 | 77 | empty |
| 2 | 507 | 0.70 | 0.80 | 52 | QM4 |
| 3 | 165 | 0.61 | 0.83 | 29 | empty |
| 4 | 147 | 0.48 | 0.78 | 28 | empty |
| 5 | 54 | 0.31 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1255 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6UZW · Crystal structure of GLUN1/GLUN2A ligand-binding domain in complex with glycine and UBP791 · the same entry in another collection · chain A against A, 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 0.98
- 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 0.90
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 6UZW · PDBe 6UZW · UniProt P35439 · UniProt Q00959
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