› 7b3j

Solution NMR

Dynamic complex between all-D-enantiomeric peptide D3 with wild-type amyloid precursor protein 672-726 fragment (amyloid beta 1-55)

Released:
DOI: 10.2210/pdb7b3j/pdb
PDB entry 7b3j coloured by chain, ensemble of 10 models, front view.
PDB entry 7b3j coloured by chain, ensemble of 10 models, side view.
PDB entry 7b3j coloured by chain, ensemble of 10 models, top view.
Source organisms:
Primary publication:
All-d-Enantiomeric Peptide D3 Designed for Alzheimer's Disease Treatment Dynamically Interacts with Membrane-Bound Amyloid-β Precursors.
Bocharov EV, Gremer L, Urban AS, Okhrimenko IS, Volynsky PE, Nadezhdin KD, Bocharova OV, Kornilov DA, Zagryadskaya YA, Kamynina AV, Kuzmichev PK, Kutzsche J, Bolakhrif N, Müller-Schiffmann A, Dencher NA, Arseniev AS, Efremov RG, Gordeliy VI, Willbold D
J Med Chem 64 16464-16479 (2021)
PMID: 34739758

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-138369 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Gamma-secretase C-terminal fragment 57 Chain: A
Molecule details ›
Chain: A
Length: 55 amino acids
Theoretical weight: 5.99 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P05067 (Residues: 672-726; Coverage: 7%)
Gene names: A4, AD1, APP
Sequence domains: Beta-amyloid peptide (beta-APP)
D3 all D-enantimeric peptide Chain: B
Molecule details ›
Chain: B
Length: 12 amino acids
Theoretical weight: 1.61 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
6 modified residues:
Ligand DAR 5 x DAR
Ligand DPR 1 x DPR
Ligand 2TL 2 x 2TL
Ligand DLE 1 x DLE
Ligand DHI 2 x DHI
Ligand DSG 1 x DSG

Experiments and Validation Details

Entry percentile scores
Chemical shift assignment: 96%
Refinement method: molecular dynamics
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

3 review citations

On the utility of microfluidic systems to study protein interactions: advantages, challenges, and applications.
Watkin et al. (2022)
2 more

1 mention without citation

In-silico structural analysis of Heterocephalus glaber amyloid beta: an anti-Alzheimer's peptide.
Javanmard et al. (2024)