2AIQ

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.191
R-Value Work: 0.168
R-Value Observed: 0.169

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

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 Biol Chem 280: 39309-39315

PubMed: 16162508 Search on PubMed
DOI: https://doi.org/10.1074/jbc.M508502200
Primary Citation of 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-).

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09872
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]
BEN Query on BEN Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	BENZAMIDINE C₇ H₈ N₂ PXXJHWLDUBFPOL-UHFFFAOYSA-N		Interactions Focus chain H [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.191
R-Value Work: 0.168
R-Value Observed: 0.169
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-09-06

Deposition Author(s):

Murakami, M.T.

Arni, R.K.

Revision History (Full details and data files)

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