1BDA | pdb_00001bda

CATALYTIC DOMAIN OF HUMAN SINGLE CHAIN TISSUE PLASMINOGEN ACTIVATOR IN COMPLEX WITH DANSYL-EGR-CMK (DANSYL-GLU-GLY-ARG CHLOROMETHYL KETONE)

• PDB DOI: https://doi.org/10.2210/pdb1BDA/pdb

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


• Deposited: 1998-05-07 Released: 1999-05-11 
• Deposition Author(s): Bode, W., Renatus, M., Engh, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å

Starting Model: experimental

Literature

Lysine 156 promotes the anomalous proenzyme activity of tPA: X-ray crystal structure of single-chain human tPA.

Renatus, M., Engh, R.A., Stubbs, M.T., Huber, R., Fischer, S., Kohnert, U., Bode, W.

(1997) EMBO J 16: 4797-4805

• PubMed: 9305622 
• DOI: https://doi.org/10.1093/emboj/16.16.4797
• Primary Citation Related Structures: 
  1BDA


• PubMed Abstract: 
  

  Tissue type plasminogen activator (tPA) is the physiological initiator of fibrinolysis, activating plasminogen via highly specific proteolysis; plasmin then degrades fibrin with relatively broad specificity. Unlike other chymotrypsin family serine proteinases, tPA is proteolytically active in a single-chain form. This form is also preferred for therapeutic administration of tPA in cases of acute myocardial infarction. The proteolytic cleavage which activates most other chymotrypsin family serine proteinases increases the catalytic efficiency of tPA only 5- to 10-fold. The X-ray crystal structure of the catalytic domain of recombinant human single-chain tPA shows that Lys156 forms a salt bridge with Asp194, promoting an active conformation in the single-chain form. Comparisons with the structures of other serine proteinases that also possess Lys156, such as trypsin, factor Xa and human urokinase plasminogen activator (uPA), identify a set of secondary interactions which are required for Lys156 to fulfil this activating role. These findings help explain the anomalous single-chain activity of tPA and may suggest strategies for design of new therapeutic plasminogen activators.

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Organizational Affiliation: 
• Max-Planck-Institute of Biochemistry, Department of Structural Research, Martinsried, Germany. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 60.71 kDa 
• Atom Count: 4,271 
• Modeled Residue Count: 530 
• Deposited Residue Count: 530 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SINGLE CHAIN TISSUE TYPE PLASMINOGEN ACTIVATOR	A, B	265	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2Z0	C [auth A], D [auth B]	N-{[5-(dimethylamino)naphthalen-2-yl]sulfonyl}-L-alpha-glutamyl-N-[(1S)-4-{[amino(iminio)methyl]amino}-1-(chloroacetyl) butyl]glycinamide C26 H37 Cl N7 O7 S VKQAIOBCWDJDIP-PMACEKPBSA-O

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000413 (2Z0)	C [auth A], D [auth B]	dansylglutamyl-glycyl-arginine chloromethyl ketone	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.99	α = 90
b = 80.78	β = 90
c = 159.16	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
ROTAGR	data reduction
X-PLOR	model building
X-PLOR	refinement
ROTAGR	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-05-11 
Deposition Author(s): Bode, W., Renatus, M., Engh, R.A.

Revision History  

• Version 1.0: 1999-05-11
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other
• Version 1.4: 2023-08-02
  Changes: Database references, Derived calculations, Refinement description, Structure summary
• Version 1.5: 2024-10-16
  Changes: Data collection, Structure summary