1BQY

Plasminogen activator (TSV-PA) from snake venom

• PDB DOI: https://doi.org/10.2210/pdb1BQY/pdb

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


• Deposited: 1998-08-20 Released: 1999-08-20 
• Deposition Author(s): Parry, M.A.A., Bode, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.258 
• R-Value Work: 0.178 
• R-Value Observed: 0.178 

Literature

The crystal structure of the novel snake venom plasminogen activator TSV-PA: a prototype structure for snake venom serine proteinases.

Parry, M.A., Jacob, U., Huber, R., Wisner, A., Bon, C., Bode, W.

(1998) Structure 6: 1195-1206

• PubMed: 9753698 
• DOI: https://doi.org/10.1016/s0969-2126(98)00119-1
• Primary Citation of Related Structures:  
  1BQY


• PubMed Abstract: 
  

  Trimeresurus stejnejeri venom plasminogen activator (TSV-PA) is a snake venom serine proteinase that specifically activates plasminogen. Snake venom serine proteinases form a subfamily of trypsin-like proteinases that are characterised by a high substrate specificity and resistance to inhibition. Many of these venom enzymes specifically interfere with haemostatic mechanisms and display a long circulating half-life. For these reasons several of them have commercial applications and are potentially attractive pharmacological tools.

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Organizational Affiliation: 

Max-Planck Institute of Biochemistry Department for Structural Research Am Klopferspitz 18a, 82152, Martinsried, Germany [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 52.06 kDa 
• Atom Count: 3,806 
• Modelled Residue Count: 468 
• Deposited Residue Count: 468 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PLASMINOGEN ACTIVATOR	A, B	234	Trimeresurus stejnegeri	Mutation(s): 0
UniProt
Find proteins for Q91516 (Trimeresurus stejnegeri) Explore Q91516  Go to UniProtKB:  Q91516

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0GJ	C [auth A], D [auth B]	L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide C14 H28 Cl N6 O5 XELWNHKFCNMWQO-LPEHRKFASA-O

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000288 (0GJ)	C [auth A], D [auth B]	GLU-GLY-ARG-CHLOROMETHYL KETONE	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.258 
• R-Value Work: 0.178 
• R-Value Observed: 0.178 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.29	α = 90
b = 67.42	β = 90
c = 163.67	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
X-PLOR	model building
X-PLOR	refinement
CCP4	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-08-20 
Deposition Author(s): Parry, M.A.A., Bode, W.

Revision History  

• Version 1.0: 1999-08-20
  Type: Initial release
  
• Version 1.1: 2008-03-24
  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: 2013-02-27
  Changes: Other
• Version 1.4: 2023-08-09
  Changes: Database references, Derived calculations, Refinement description