MolNFT v1 · #97494 · protein
Crystal structure of the NMDA receptor GLUN1 ligand binding domain in complex with 1-thioxo-1,2-dihydro-[1,2,4]TRIAZOLO[4,3-A]QUINOXALIN- 4(5H)-one
4KFQ · Glutamate receptor ionotropic, NMDA 1: “Crystal structure of the NMDA receptor GLUN1 ligand binding domain in complex with…”. X-ray diffraction, 2 ligands (KFQ, SO4), 6 pockets (best druggability 0.72). MolNFT v1 #97494 on…
- PDB
- 4KFQ
- Type
- protein
- Length
- 571 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, NMDA 1
- UniProt
- P35439
- Ligands
- KFQ, SO4
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, NMDA 1 | protein | 289 | 31% helix, 28% strand | P35439 |
| B | Glutamate receptor ionotropic, NMDA 1 | protein | 282 | 32% helix, 28% strand | P35439 |
Ligands and binding sites
- KFQ · 1-sulfanyl[1,2,4]triazolo[4,3-a]quinoxalin-4(5H)-one · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- GOL · Glycerol · additive · 18 copies · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 643 | 0.72 | 0.79 | 58 | KFQ, GOL |
| 2 | 547 | 0.69 | 0.79 | 57 | KFQ, GOL |
| 3 | 190 | 0.43 | 0.73 | 34 | GOL |
| 4 | 68 | 0.34 | 0.76 | 17 | GOL |
| 5 | 74 | 0.34 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 328 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4KFQ · Crystal structure of the NMDA receptor GluN1 ligand binding domain in complex with… · 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 B against A, TM-score 0.93
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
- Elsewhere: RCSB PDB 4KFQ · PDBe 4KFQ · UniProt P35439
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