2AIQ | pdb_00002aiq

Crystal structure of benzamidine-inhibited protein C activator from the venom of copperhead snake Agkistrodon contortrix contortrix

• PDB DOI: https://doi.org/10.2210/pdb2AIQ/pdb

• Classification: HYDROLASE
• Organism(s): Agkistrodon contortrix contortrix
• Mutation(s): No 


• Deposited: 2005-07-30 Released: 2005-09-06 
• Deposition Author(s): Murakami, M.T., Arni, R.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.191 (Depositor), 0.169 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Thrombomodulin-independent Activation of Protein C and Specificity of Hemostatically Active Snake Venom Serine Proteinases: CRYSTAL STRUCTURES OF NATIVE AND INHIBITED AGKISTRODON CONTORTRIX CONTORTRIX PROTEIN C ACTIVATOR.

Murakami, M.T., Arni, R.K.

(2005) J Biological Chem 280: 39309-39315

• PubMed: 16162508 
• DOI: https://doi.org/10.1074/jbc.M508502200
• Primary Citation Related Structures: 
  2AIP, 2AIQ


• PubMed Abstract: 
  

  Protein C activation initiated by the thrombin-thrombomodulin complex forms the major physiological anticoagulant pathway. Agkistrodon contortrix contortrix protein C activator, a glycosylated single-chain serine proteinase, activates protein C without relying on thrombomodulin. The crystal structures of native and inhibited Agkistrodon contortrix contortrix protein C activator determined at 1.65 and 1.54 A resolutions, respectively, indicate the pivotal roles played by the positively charged belt and the strategic positioning of the three carbohydrate moieties surrounding the catalytic site in protein C recognition, binding, and activation. Structural changes in the benzamidine-inhibited enzyme suggest a probable function in allosteric regulation for the anion-binding site located in the C-terminal extension, which is fully conserved in snake venom serine proteinases, that preferentially binds Cl(1-) instead of SO(4)(2-).

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Organizational Affiliation: 
• Biochemistry and Structural Biology Group, Department of Physics, IBILCE/UNESP, São José do Rio Preto, SP 15054-000, Brazil.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 26.2 kDa 
• Atom Count: 2,067 
• Modeled Residue Count: 231 
• Deposited Residue Count: 231 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein C activator	A	231	Agkistrodon contortrix contortrix	Mutation(s): 0  EC: 3.4.21.74 (PDB Primary Data), 3.4.21 (UniProt)
UniProt
Find proteins for P09872 (Agkistrodon contortrix contortrix) Explore P09872  Go to UniProtKB:  P09872
Glycosylation
Glycosylation Sites: 3

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A], C [auth A], D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
BEN	H [auth A]	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free:  0.191 (Depositor), 0.169 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.516	α = 90
b = 63.463	β = 99.85
c = 48.216	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-06 
Deposition Author(s): Murakami, M.T., Arni, R.K.

Revision History  

• Version 1.0: 2005-09-06
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-08-23
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-06
  Changes: Structure summary