Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 58.75 kDa 
• Atom Count: 4213 
• Residue Count: 518 
• Unique protein chains: 2

1A5H

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

• DOI: 10.2210/pdb1A5H/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-02-17 Released: 1999-04-20 
• Deposition Author(s): Renatus, M., Bode, W., Stubbs, M.T.

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Experimental Data Snapshot

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

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

• PubMed: 9268299 
• 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-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.

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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

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Organizational Affiliation: 

Max Planck Institute of Biochemistry, Department of Structural Research, D-82152 Martinsried, Germany. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TISSUE PLASMINOGEN ACTIVATOR	C, D	7	Homo sapiens	Mutation(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 GTEx  ENSG00000104368

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TISSUE PLASMINOGEN ACTIVATOR	A, B	252	Homo sapiens	Mutation(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 GTEx  ENSG00000104368

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BBA	A, B	2,7-BIS-(4-AMIDINOBENZYLIDENE)-CYCLOHEPTAN-1-ONE C23 H28 N4 O BXYGSMRTHHSAHZ-PMACEKPBSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
BBA	Ki :  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 = 151.83	α = 90
b = 60.5	β = 110.5
c = 62.61	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
XSCALE	data scaling
X-PLOR	model building
X-PLOR	refinement
XDS	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-02-17 
• Released Date: 1999-04-20 
Deposition Author(s): Renatus, M., Bode, W., Stubbs, M.T.

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