MolNFT v1 · #121768 · protein
Agonist-bound GLUN1/GLUN2A agonist binding domains with TCN201
5I56 · Glutamate receptor ionotropic, NMDA 1,GLUTAMATE receptor…: “Agonist-bound GLUN1/GLUN2A agonist binding domains with TCN201”. X-ray diffraction, 3 ligands (GLY, GLU, 67P), 6 pockets (best druggability 0.81). MolNFT v1 #121768 on…
- PDB
- 5I56
- Type
- protein
- Length
- 566 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
- GLY, GLU, 67P
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, NMDA 1,GLUTAMATE receptor ionotropic, NMDA 1 | protein | 286 | 31% helix, 27% strand | P35439 |
| B | Glutamate receptor ionotropic, NMDA 2A,GLUTAMATE receptor ionotropic, NMDA 2A | protein | 280 | 32% helix, 26% strand | Q00959 |
Ligands and binding sites
- GLY · Glycine · ligand · chains A
- GLU · Glutamic acid · ligand · chains B
- 67P · N-({4-[2-(benzenecarbonyl)hydrazinecarbonyl]phenyl}methyl)-3-chloro-4-fluorobenzene-1-sulfonamide · ligand · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1140 | 0.81 | 0.82 | 122 | 67P |
| 2 | 226 | 0.62 | 0.82 | 37 | empty |
| 3 | 73 | 0.58 | 0.89 | 23 | GLU |
| 4 | 80 | 0.57 | 0.87 | 27 | empty |
| 5 | 70 | 0.37 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1141 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5I56 · Agonist-bound GluN1/GluN2A agonist binding domains with TCN201 · 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 5I56 · PDBe 5I56 · UniProt P35439 · UniProt Q00959
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