3NCL: Crystal Structure of Mt-sp1 Bound to Benzamidine Phosphonate Inhibitor

The ability to follow enzyme activity in a cellular context represents a challenging technological frontier that impacts fields ranging from disease pathogenesis to epigenetics. Activity-based probes (ABPs) label the active form of an enzyme via covalent modification of catalytic residues. Here we present an analysis of parameters influencing potency of peptide phosphonate ABPs for trypsin-fold S1A proteases, an abundant and important class of enzymes with similar substrate specificities. We find that peptide length and stability influence potency more than sequence composition and present structural evidence that steric interactions at the prime-side of the substrate-binding cleft affect potency in a protease-dependent manner. We introduce guidelines for the design of peptide phosphonate ABPs and demonstrate their utility in a live-cell labeling application that specifically targets active S1A proteases at the cell surface of cancer cells.
PDB ID: 3NCLDownload
MMDB ID: 88669
PDB Deposition Date: 2010/6/4
Updated in MMDB: 2011/05 
Experimental Method:
x-ray diffraction
Resolution: 1.19  Å
Source Organism:
Similar Structures:
Biological Unit for 3NCL: monomeric; determined by author and by software (PISA)
Molecular Components in 3NCL
Label Count Molecule
Protein (1 molecule)
Suppressor of Tumorigenicity 14 Protein
Molecule annotation
Chemicals (4 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB