› 6t0p

X-ray diffraction
1.19Å resolution

Cationic Trypsin in Complex with a D-Phe-Pro-2-aminopyridine derivative

Released:
DOI: 10.2210/pdb6t0p/pdb
PDB entry 6t0p coloured by chain, front view.
PDB entry 6t0p coloured by chain, side view.
PDB entry 6t0p coloured by chain, top view.
Source organism: Bos taurus
Primary publication:
Protein-Induced Change in Ligand Protonation during Trypsin and Thrombin Binding: Hint on Differences in Selectivity Determinants of Both Proteins?
Ngo K, Collins-Kautz C, Gerstenecker S, Wagner B, Heine A, Klebe G
J Med Chem 63 3274-3289 (2020)
PMID: 32011145

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133319 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Serine protease 1 Chain: A
Molecule details ›
Chain: A
Length: 246 amino acids
Theoretical weight: 25.81 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P00760 (Residues: 1-246; Coverage: 100%)
Gene names: PRSS1, TRP1, TRY1, TRYP1
Sequence domains: Trypsin

Ligands and Environments

4 bound ligands:
Ligand CA 1 x CA
Ligand DMS 2 x DMS
Ligand M6Q 1 x M6Q
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)
Spacegroup: P212121
Unit cell:
a: 54.568Å b: 56.684Å c: 66.647Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.124 0.123 0.138

Quick links

Citations

1 citations in other articles

Two Methods, One Goal: Structural Differences between Cocrystallization and Crystal Soaking to Discover Ligand Binding Poses.
Wienen-Schmidt et al. (2021)