› 6dmi

X-ray diffraction
1.9Å resolution

A multiconformer ligand model of 5T5 bound to BACE-1

Released:
DOI: 10.2210/pdb6dmi/pdb
PDB entry 6dmi coloured by chain, front view.
PDB entry 6dmi coloured by chain, side view.
PDB entry 6dmi coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps.
van Zundert GCP, Hudson BM, de Oliveira SHP, Keedy DA, Fonseca R, Heliou A, Suresh P, Borrelli K, Day T, Fraser JS, van den Bedem H
J Med Chem 61 11183-11198 (2018)
PMID: 30457858

Function and Biology Details

Reaction catalysed: 
Broad endopeptidase specificity. Cleaves Glu-Val-Asn-Leu-|-Asp-Ala-Glu-Phe in the Swedish variant of Alzheimer's amyloid precursor protein.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-157541 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Beta-secretase 1 Chain: A
Molecule details ›
Chain: A
Length: 390 amino acids
Theoretical weight: 43.41 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P56817 (Residues: 57-446; Coverage: 81%)
Gene names: BACE, BACE1, KIAA1149
Sequence domains: Eukaryotic aspartyl protease
Structure domains: Acid Proteases

Ligands and Environments

3 bound ligands:
Ligand NA 2 x NA
Ligand DMS 1 x DMS
Ligand 5T5 1 x 5T5
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P6122
Unit cell:
a: 102.32Å b: 102.32Å c: 169.82Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.194 0.192 0.226
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Advances in methods for atomic resolution macromolecular structure determination.
Thompson et al. (2020)
24 other articles

1 mention without citation

qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps.
van Zundert et al. (2018)