› 5qd1

X-ray diffraction
2.4Å resolution

Crystal structure of BACE complex with BMC011

Released:
DOI: 10.2210/pdb5qd1/pdb
PDB entry 5qd1 coloured by chain, front view.
PDB entry 5qd1 coloured by chain, side view.
PDB entry 5qd1 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.
Parks CD, Gaieb Z, Chiu M, Yang H, Shao C, Walters WP, Jansen JM, McGaughey G, Lewis RA, Bembenek SD, Ameriks MK, Mirzadegan T, Burley SK, Amaro RE, Gilson MK
J Comput Aided Mol Des 34 99-119 (2020)
PMID: 31974851

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 Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 402 amino acids
Theoretical weight: 44.78 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P56817 (Residues: 48-447; Coverage: 83%)
Gene names: BACE, BACE1, KIAA1149
Sequence domains: Eukaryotic aspartyl protease

Ligands and Environments

1 bound ligand:
Ligand E61 3 x E61
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E
Spacegroup: P21
Unit cell:
a: 82.849Å b: 104.217Å c: 100.832Å
α: 90° β: 104.37° γ: 90°
R-values:
R R work R free
0.166 0.163 0.197
Expression system: Escherichia coli

Quick links

Citations

10 review citations

Protein storytelling through physics.
Brini et al. (2020)
9 more