4ZHM

The crystal structure of mupain-1--16-IG in complex with murinised human uPA at pH7.4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Selection of High-Affinity Peptidic Serine Protease Inhibitors with Increased Binding Entropy from a Back-Flip Library of Peptide-Protease Fusions.

Srensen, H.P.Xu, P.Jiang, L.Kromann-Hansen, T.Jensen, K.J.Huang, M.Andreasen, P.A.

(2015) J.Mol.Biol. 427: 3110-3122

  • DOI: 10.1016/j.jmb.2015.08.005
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We have developed a new concept for designing peptidic protein modulators, by recombinantly fusing the peptidic modulator, with randomized residues, directly to the target protein via a linker and screening for internal modulation of the activity of ...

    We have developed a new concept for designing peptidic protein modulators, by recombinantly fusing the peptidic modulator, with randomized residues, directly to the target protein via a linker and screening for internal modulation of the activity of the protein. We tested the feasibility of the concept by fusing a 10-residue-long, disulfide-bond-constrained inhibitory peptide, randomized in selected positions, to the catalytic domain of the serine protease murine urokinase-type plasminogen activator. High-affinity inhibitory peptide variants were identified as those that conferred to the fusion protease the lowest activity for substrate hydrolysis. The usefulness of the strategy was demonstrated by the selection of peptidic inhibitors of murine urokinase-type plasminogen activator with a low nanomolar affinity. The high affinity could not have been predicted by rational considerations, as the high affinity was associated with a loss of polar interactions and an increased binding entropy.


    Organizational Affiliation

    Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
mupain-1-16-IG
P
10N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Urokinase-type plasminogen activator
U
247Homo sapiensMutation(s): 3 
Gene Names: PLAU
EC: 3.4.21.73
Find proteins for P00749 (Homo sapiens)
Go to Gene View: PLAU
Go to UniProtKB:  P00749
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MRZ
Query on MRZ

Download SDF File 
Download CCD File 
P
piperidine-1-carboximidamide
C6 H13 N3
QUUYRYYUKNNNNS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.223 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 120.897α = 90.00
b = 120.897β = 90.00
c = 42.311γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data processing
REFMACrefinement
HKL-2000data scaling
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-16
    Type: Initial release
  • Version 1.1: 2015-10-14
    Type: Database references