MolNFT v1 · #166740 · protein
Crystal structure of GLUN1/GLUN2A-4M mutant ligand-binding domain in complex with glycine and homoquinolinic acid
6UZG · Glutamate receptor ionotropic, NMDA 1: “Crystal structure of GLUN1/GLUN2A-4M mutant ligand-binding domain in complex with glycine and homoquinolinic…”. X-ray diffraction, 2 ligands (GLY, QM1), 6 pockets (best druggability 0.80).…
- PDB
- 6UZG
- Type
- protein
- Length
- 565 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, QM1
- Pockets
- 6 · best druggability 0.80
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 | 285 | 31% helix, 26% strand | P35439 |
| B | Glutamate receptor ionotropic, NMDA 2A | protein | 280 | 34% helix, 26% strand | Q00959 |
Ligands and binding sites
- GLY · Glycine · ligand · chains A
- QM1 · 3-(carboxymethyl)pyridine-2-carboxylic 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 | 1027 | 0.80 | 0.81 | 110 | empty |
| 2 | 208 | 0.58 | 0.80 | 34 | empty |
| 3 | 94 | 0.57 | 0.86 | 25 | empty |
| 4 | 60 | 0.41 | 0.81 | 17 | empty |
| 5 | 120 | 0.38 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1209 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6UZG · Crystal structure of GLUN1/GLUN2A-4M mutant ligand-binding domain in complex with glycine… · 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 6UZG · PDBe 6UZG · UniProt P35439 · UniProt Q00959
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.