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 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: 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-nitr ...

    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.


    Related Citations: 
    • Tissue-Type Plasminogen Activator: Variants and Crystal/Solution Structures Demarcate Structural Determinants of Function
      Bode, W., Renatus, M.
      (1997) Curr Opin Struct Biol 7: 865
    • The 2.3 A Crystal Structure of the Catalytic Domain of Recombinant Two-Chain Human Tissue-Type Plasminogen Activator
      Lamba, D., Bauer, M., Huber, R., Fischer, S., Rudolph, R., Kohnert, U., Bode, W.
      (1996) J Mol Biol 258: 117

    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   |   Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TISSUE PLASMINOGEN ACTIVATORCD7Homo sapiensMutation(s): 0 
Gene Names: PLAT
EC: 3.4.21.68
Find proteins for P00750 (Homo sapiens)
Explore P00750 
Go to UniProtKB:  P00750
NIH Common Fund Data Resources
PHAROS  P00750
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TISSUE PLASMINOGEN ACTIVATORAB252Homo sapiensMutation(s): 0 
Gene Names: PLAT
EC: 3.4.21.68
Find proteins for P00750 (Homo sapiens)
Explore P00750 
Go to UniProtKB:  P00750
NIH Common Fund Data Resources
PHAROS  P00750
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BBA
Query on BBA

Download Ideal Coordinates CCD File 
A, B
2,7-BIS-(4-AMIDINOBENZYLIDENE)-CYCLOHEPTAN-1-ONE
C23 H28 N4 O
BXYGSMRTHHSAHZ-PMACEKPBSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BBAKi :  500   nM  PDBBind
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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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