6A8N | pdb_00006a8n

The crystal structure of muPAin-1-IG-2 in complex with muPA-SPD at pH8.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 
    0.256 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Suppression of Tumor Growth and Metastases by Targeted Intervention in Urokinase Activity with Cyclic Peptides.

Wang, D.Yang, Y.Jiang, L.Wang, Y.Li, J.Andreasen, P.A.Chen, Z.Huang, M.Xu, P.

(2019) J Med Chem 62: 2172-2183

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b01908
  • Primary Citation Related Structures: 
    6A8G, 6A8N

  • PubMed Abstract: 

    Urokinase-type plasminogen activator (uPA) is a diagnostic marker for breast and prostate cancers recommended by American Society for Clinical Oncology and German Breast Cancer Society. Inhibition of uPA was proposed as an efficient strategy for cancer treatments. In this study, we report peptide-based uPA inhibitors with high potency and specificity comparable to monoclonal antibodies. We revealed the binding and inhibitory mechanisms by combining crystallography, molecular dynamic simulation, and other biophysical and biochemical approaches. Besides, we showed that our peptides efficiently inhibited the invasion of cancer cells via intervening with the processes of the degradation of extracellular matrices. Furthermore, our peptides significantly suppressed the tumor growth and the cancer metastases in tumor-bearing mice. This study demonstrates that these uPA peptides are highly potent anticancer agents and reveals the mechanistic insights of these uPA inhibitors, which can be useful for developing other serine protease inhibitors.


  • Organizational Affiliation
    • State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter , Chinese Academy of Sciences , 155 West Yangqiao Road , Fuzhou , Fujian 350002 , China.

Macromolecule Content 

  • Total Structure Weight: 57.37 kDa 
  • Atom Count: 4,006 
  • Modeled Residue Count: 510 
  • Deposited Residue Count: 514 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Urokinase-type plasminogen activator BA,
C [auth B]
247Mus musculusMutation(s): 1 
Gene Names: Plau
EC: 3.4.21.73
UniProt & NIH Common Fund Data Resources
Find proteins for P06869 (Mus musculus)
Explore P06869 
Go to UniProtKB:  P06869
IMPC:  MGI:97611
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06869
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
CYS-PRO-ALA-TYR-SER-ARG-TYR-ILE-GLY-CYSB [auth P],
D [auth C]
10Phage display vector pTDispMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free:  0.256 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.028α = 90
b = 112.028β = 90
c = 102.214γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina21708043
National Natural Science Foundation of ChinaChina81572944
National Natural Science Foundation of ChinaChinaU1405229

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2019-09-04
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary