Research workbench
Structure of the human GLUN1/GLUN2A lbd in complex with GNE0723
Analyse Structure of the human GLUN1/GLUN2A lbd in complex with GNE0723 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KDT
- Type
- protein
- Length
- 562 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor ionotropic, NMDA 2A; Glutamate receptor ionotropic, NMDA 1
- UniProt
- Q12879, Q05586
- Ligands
- GLU, 6RV, GLY
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, NMDA 2A | protein | 278 | 34% helix, 26% strand | Q12879 |
| B | Glutamate receptor ionotropic, NMDA 1 | protein | 284 | 30% helix, 27% strand | Q05586 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · chains A
- 6RV · (1~{R},2~{R})-2-[7-[[5-chloranyl-3-(trifluoromethyl) pyrazol-1-yl]methyl]-5-oxidanylidene-2-(trifluoromethyl)-[1,3]thiazolo[3,2-a]pyrimidin-3-yl]cyclopropane-1-carbonitrile · ligand · chains A, B
- GLY · Glycine · ligand · chains B
- ACT · Acetate ion · additive · chains A
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 | 699 | 0.78 | 0.83 | 87 | 6RV |
| 2 | 258 | 0.60 | 0.80 | 35 | empty |
| 3 | 246 | 0.58 | 0.79 | 28 | empty |
| 4 | 63 | 0.56 | 0.89 | 20 | GLU |
| 5 | 61 | 0.31 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1124 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5KDT · Structure of the human GluN1/GluN2A LBD in complex with GNE0723 · the same entry in another collection · chain A against A, TM-score 1.00
- Q12879 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 2A (Q12879) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q05586 · AlphaFold monomer V2.0 prediction for glutamate receptor ionotropic, NMDA 1 (Q05586) · a predicted model of the same protein · chain B 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 Q12879
- Every structure of UniProt Q05586
- Elsewhere: RCSB PDB 5KDT · PDBe 5KDT · UniProt Q12879 · UniProt Q05586
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