› 5jbt

X-ray diffraction
1.4Å resolution

Mesotrypsin in complex with cleaved amyloid precursor like protein 2 inhibitor (APLP2)

Released:
DOI: 10.2210/pdb5jbt/pdb
PDB entry 5jbt coloured by chain, front view.
PDB entry 5jbt coloured by chain, side view.
PDB entry 5jbt coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
An Acrobatic Substrate Metamorphosis Reveals a Requirement for Substrate Conformational Dynamics in Trypsin Proteolysis.
Kayode O, Wang R, Pendlebury DF, Cohen I, Henin RD, Hockla A, Soares AS, Papo N, Caulfield TR, Radisky ES
J Biol Chem 291 26304-26319 (2016)
PMID: 27810896

Function and Biology Details

Reaction catalysed: 
Preferential cleavage: Arg-|-, Lys-|-.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152774 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Trypsin-3 Chain: A
Molecule details ›
Chain: A
Length: 224 amino acids
Theoretical weight: 24.26 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P35030 (Residues: 81-304; Coverage: 74%)
Gene names: PRSS3, PRSS4, TRY3, TRY4
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases
Amyloid beta precursor like protein 2 Chain: X
Molecule details ›
Chain: X
Length: 14 amino acids
Theoretical weight: 1.48 KDa
Source organism: Homo sapiens
Expression system: Komagataella pastoris
UniProt:
  • Canonical: Q06481 (Residues: 307-320; Coverage: 2%)
Gene names: APLP2, APPL2
Amyloid beta precursor like protein 2 Chain: Y
Molecule details ›
Chain: Y
Length: 38 amino acids
Theoretical weight: 4.42 KDa
Source organism: Homo sapiens
Expression system: Komagataella pastoris
UniProt:
  • Canonical: Q06481 (Residues: 323-360; Coverage: 5%)
Gene names: APLP2, APPL2
Sequence domains: Kunitz/Bovine pancreatic trypsin inhibitor domain

Ligands and Environments

2 bound ligands:
Ligand CA 1 x CA
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P21212
Unit cell:
a: 98.956Å b: 54.539Å c: 56.632Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.165 0.163 0.198
Expression systems:
  • Escherichia coli BL21(DE3)
  • Komagataella pastoris

Quick links

Citations

2 review citations

Apolipoprotein E and Alzheimer disease: pathobiology and targeting strategies.
Yamazaki et al. (2019)
1 more

1 mention without citation

An Acrobatic Substrate Metamorphosis Reveals a Requirement for Substrate Conformational Dynamics in Trypsin Proteolysis.
Kayode et al. (2016)