3BN9

Crystal Structure of MT-SP1 in complex with Fab Inhibitor E2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.173 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of an Fab-protease complex reveals a highly specific non-canonical mechanism of inhibition

Farady, C.J.Egea, P.F.Schneider, E.L.Darragh, M.R.Craik, C.S.

(2008) J.Mol.Biol. 380: 351-360

  • DOI: 10.1016/j.jmb.2008.05.009

  • PubMed Abstract: 
  • The vast majority of protein protease inhibitors bind their targets in a substrate-like manner. This is a robust and efficient mechanism of inhibition but, due to the highly conserved architecture of protease active sites, these inhibitors often exhi ...

    The vast majority of protein protease inhibitors bind their targets in a substrate-like manner. This is a robust and efficient mechanism of inhibition but, due to the highly conserved architecture of protease active sites, these inhibitors often exhibit promiscuity. Inhibitors that show strict specificity for one protease usually achieve this selectivity by combining substrate-like binding in the active site with exosite binding on the protease surface. The development of new, specific inhibitors can be aided greatly by binding to non-conserved regions of proteases if potency can be maintained. Due to their ability to bind specifically to nearly any antigen, antibodies provide an excellent scaffold for creating inhibitors targeted to a single member of a family of highly homologous enzymes. The 2.2 A resolution crystal structure of an Fab antibody inhibitor in complex with the serine protease membrane-type serine protease 1 (MT-SP1/matriptase) reveals the molecular basis of its picomolar potency and specificity. The inhibitor has a distinct mechanism of inhibition; it gains potency and specificity through interactions with the protease surface loops, and inhibits by binding in the active site in a catalytically non-competent manner. In contrast to most naturally occurring protease inhibitors, which have diverse structures but converge to a similar inhibitory archetype, antibody inhibitors provide an opportunity to develop divergent mechanisms of inhibition from a single scaffold.


    Organizational Affiliation

    Graduate Group in Biophysics, University of California, San Francisco, 600 16th St. Genentech Hall, San Francisco, CA 94143-2240, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Membrane-type serine protease 1
B, A
241Homo sapiensGene Names: ST14 (PRSS14, SNC19, TADG15)
EC: 3.4.21.109
Find proteins for Q9Y5Y6 (Homo sapiens)
Go to Gene View: ST14
Go to UniProtKB:  Q9Y5Y6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
E2 Fab Light Chain
C, E
214N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
E2 Fab Heavy Chain
D, F
257Homo sapiensGene Names: IGHV3-23
Find proteins for P01764 (Homo sapiens)
Go to UniProtKB:  P01764
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
C, E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C, D, E
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.173 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.625α = 90.00
b = 163.279β = 90.00
c = 201.160γ = 90.00
Software Package:
Software NamePurpose
ELVESdata reduction
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Advisory, Refinement description, Source and taxonomy