MolNFT v1 · #123755 · protein
Glutamate- and dcka-bound GLUN1/GLUN2A agonist binding domains with mpx-007
5JTY · Glutamate receptor ionotropic, NMDA 1,GLUTAMATE receptor…: “Glutamate- and dcka-bound GLUN1/GLUN2A agonist binding domains with mpx-007”. X-ray diffraction, 3 ligands (2JK, 6ND, GLU), 6 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 5JTY
- Type
- protein
- Length
- 538 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 1; Glutamate…
- UniProt
- P35439, Q00959
- Ligands
- 2JK, 6ND, GLU
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, NMDA 1,GLUTAMATE receptor ionotropic, NMDA 1 | protein | 262 | 32% helix, 27% strand | P35439 |
| B | Glutamate receptor ionotropic, NMDA 2A,GLUTAMATE receptor ionotropic, NMDA 2A | protein | 276 | 33% helix, 26% strand | Q00959 |
Ligands and binding sites
- 2JK · 4-hydroxy-5,7-dimethylquinoline-2-carboxylic acid · ligand · chains A
- 6ND · 5-({[(3,4-difluorophenyl)sulfonyl]amino}methyl)-6-methyl-N-[(2-methyl-1,3-thiazol-5-yl)methyl]pyrazine-2-carboxamide · ligand · chains A, B
- GLU · Glutamic 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1024 | 0.84 | 0.85 | 106 | 2JK, 6ND |
| 2 | 183 | 0.63 | 0.84 | 30 | empty |
| 3 | 62 | 0.60 | 0.91 | 19 | GLU |
| 4 | 88 | 0.50 | 0.83 | 24 | empty |
| 5 | 89 | 0.35 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1250 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5JTY · Glutamate- and DCKA-bound GluN1/GluN2A agonist binding domains with MPX-007 · 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 0.97
- 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 0.92
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 5JTY · PDBe 5JTY · UniProt P35439 · UniProt Q00959
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