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: 1.90 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

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:  
    4ZHL, 4ZHM

  • 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 the protein ...

    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; Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 350002 Fuzhou, People's Republic of China. Electronic address: pa@mbg.au.dk.



Macromolecules
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
mupain-1-16-IGA [auth P]10synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Urokinase-type plasminogen activatorB [auth U]247Homo sapiensMutation(s): 3 
Gene Names: PLAU
EC: 3.4.21.73
UniProt & NIH Common Fund Data Resources
Find proteins for P00749 (Homo sapiens)
Explore P00749 
Go to UniProtKB:  P00749
PHAROS:  P00749
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MRZ
Query on MRZ

Download Ideal Coordinates CCD File 
C [auth P]piperidine-1-carboximidamide
C6 H13 N3
QUUYRYYUKNNNNS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.897α = 90
b = 120.897β = 90
c = 42.311γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data processing
HKL-2000data scaling
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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