› 3v13

X-ray diffraction
1.63Å resolution

Bovine trypsin variant X(tripleGlu217Phe227) in complex with small molecule inhibitor

Released:
DOI: 10.2210/pdb3v13/pdb
PDB entry 3v13 coloured by chain, front view.
PDB entry 3v13 coloured by chain, side view.
PDB entry 3v13 coloured by chain, top view.
Source organism: Bos taurus
Primary publication:
Correlating structure and ligand affinity in drug discovery: a cautionary tale involving second shell residues.
Tziridis A, Rauh D, Neumann P, Kolenko P, Menzel A, Bräuer U, Ursel C, Steinmetzer P, Stürzebecher J, Schweinitz A, Steinmetzer T, Stubbs MT
Biol Chem 395 891-903 (2014)
PMID: 25003390

Function and Biology Details

Reaction catalysed: 
Preferential cleavage: Arg-|-, Lys-|-.
Biochemical function:
Biological process:
Cellular component:
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: 223 amino acids
Theoretical weight: 23.48 KDa
Source organism: Bos taurus
Expression system: Escherichia coli
UniProt:
  • Canonical: P00760 (Residues: 24-246; Coverage: 97%)
Gene names: PRSS1, TRP1, TRY1, TRYP1
Sequence domains: Trypsin
Structure domains: Trypsin-like serine proteases

Ligands and Environments

6 bound ligands:
Ligand CA 1 x CA
Ligand 3YH 1 x 3YH
Ligand SO4 3 x SO4
Ligand IMD 1 x IMD
Ligand GOL 1 x GOL
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P65
Unit cell:
a: 81.813Å b: 81.813Å c: 63.865Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.148 0.146 0.175
Expression system: Escherichia coli

Quick links

Citations

5 citation in other articles

Structure-Based Macrocyclization of Substrate Analogue NS2B-NS3 Protease Inhibitors of Zika, West Nile and Dengue viruses.
Braun et al. (2020)
4 more

1 mention without citation

SARS-CoV-2 attachment to host cells is possibly mediated via RGD-integrin interaction in a calcium-dependent manner and suggests pulmonary EDTA chelation therapy as a novel treatment for COVID 19.
Dakal TC. (2021)