Research workbench
Structure of the human GluN1/GluN2A LBD in complex with NAM
Analyse Structure of the human GluN1/GluN2A LBD in complex with NAM in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H8N
- Type
- protein
- Length
- 558 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Homo sapiens
- Molecule
- Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A; Glutamate…
- UniProt
- Q12879, Q05586
- Ligands
- GLU, 5YD, GLY, CA
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.5 · 2 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A | protein | 276 | 33% helix, 26% strand | Q12879 |
| B | Glutamate receptor ionotropic, NMDA 1,Glutamate receptor ionotropic, NMDA 1 | protein | 282 | 31% helix, 28% strand | Q05586 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · chains A
- 5YD · 4-[[(4-fluorophenyl)sulfonylamino]methyl]-~{N}-(pyridin-3-ylmethyl)benzamide · ligand · chains A, B
- GLY · Glycine · ligand · chains B
- CA · Calcium ion · metal · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 750 | 0.80 | 0.83 | 73 | 5YD |
| 2 | 199 | 0.64 | 0.84 | 30 | empty |
| 3 | 278 | 0.63 | 0.80 | 39 | empty |
| 4 | 82 | 0.58 | 0.87 | 30 | empty |
| 5 | 204 | 0.56 | 0.79 | 37 | GLU |
Interfaces
1 interface between chains.
- A–B · 1297 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5H8N · Structure of the human GLUN1/GLUN2A lbd in complex with nam · 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 5H8N · PDBe 5H8N · UniProt Q12879 · UniProt Q05586
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