1A5H

CATALYTIC DOMAIN OF HUMAN TWO-CHAIN TISSUE PLASMINOGEN ACTIVATOR COMPLEX OF A BIS-BENZAMIDINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural mapping of the active site specificity determinants of human tissue-type plasminogen activator. Implications for the design of low molecular weight substrates and inhibitors.

Renatus, M.Bode, W.Huber, R.Sturzebecher, J.Prasa, D.Fischer, S.Kohnert, U.Stubbs, M.T.

(1997) J Biol Chem 272: 21713-21719

  • DOI: https://doi.org/10.1074/jbc.272.35.21713
  • Primary Citation of Related Structures:  
    1A5H

  • PubMed Abstract: 

    The recent structure determination of the catalytic domain of tissue-type plasminogen activator (tPA) suggested residue Arg174 could play a role in P3/P4 substrate specificity. Six synthetic chromogenic tPA substrates of the type R-Xaa-Gly-Arg-p-nitroanilide, in which R is an N-terminal protection group, were synthesized to test this property. Although changing the residue Xaa (in its L or D form) at position P3 from the hydrophobic Phe to an acidic residue, Asp or Glu, gave no improvement in catalytic efficiency, comparative analysis of the substrates indicated a preference for an acidic substituent occupying the S3 site when the S4 site contains a hydrophobic or basic moiety. The 2.9 A structure determination of the catalytic domain of human tPA in complex with the bis-benzamidine inhibitor 2, 7-bis-(4-amidinobenzylidene)-cycloheptan-1-one reveals a three-site interaction, salt bridge formation of the proximal amidino group of the inhibitor with Asp189 in the primary specificity pocket, extensive hydrophobic surface burial, and a weak electrostatic interaction between the distal amidino group of the inhibitor and two carbonyl oxygens of the protein. The latter position was previously occupied by the guanidino group of Arg174, which swings out to form the western edge of the S3 pocket. These data suggest that the side chain of Arg174 is flexible, and does not play a major role in the S4 specificity of tPA. On the other hand, this residue would modulate S3 specificity, and may be exploited to fine tune the specificity and selectivity of tPA substrates and inhibitors.


  • Organizational Affiliation

    Max Planck Institute of Biochemistry, Department of Structural Research, D-82152 Martinsried, Germany. renatus@biochem.mpg.de


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TISSUE PLASMINOGEN ACTIVATORA [auth C],
C [auth D]
7Homo sapiensMutation(s): 0 
EC: 3.4.21.68
UniProt & NIH Common Fund Data Resources
Find proteins for P00750 (Homo sapiens)
Explore P00750 
Go to UniProtKB:  P00750
PHAROS:  P00750
GTEx:  ENSG00000104368 
Entity Groups  
UniProt GroupP00750
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TISSUE PLASMINOGEN ACTIVATORB [auth A],
D [auth B]
252Homo sapiensMutation(s): 0 
EC: 3.4.21.68
UniProt & NIH Common Fund Data Resources
Find proteins for P00750 (Homo sapiens)
Explore P00750 
Go to UniProtKB:  P00750
PHAROS:  P00750
GTEx:  ENSG00000104368 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00750
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BBA
Query on BBA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]
2,7-BIS-(4-AMIDINOBENZYLIDENE)-CYCLOHEPTAN-1-ONE
C23 H28 N4 O
BXYGSMRTHHSAHZ-PMACEKPBSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
BBA PDBBind:  1A5H Ki: 500 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.83α = 90
b = 60.5β = 110.5
c = 62.61γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
XSCALEdata scaling
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-04-20
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-09-05
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2023-08-02
    Changes: Advisory, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-11-06
    Changes: Data collection, Structure summary