7AHP

Crystal structure of Ixodes ricinus serpin - Iripin-3

• PDB DOI: https://doi.org/10.2210/pdb7AHP/pdb

• Classification: HYDROLASE INHIBITOR
• Organism(s): Ixodes ricinus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-09-25 Released: 2021-03-10 
• Deposition Author(s): Kascakova, B., Kuta Smatanova, I., Prudnikova, T.
• Funding Organization(s): Grant Agency of the Czech Republic

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.223 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 

Literature

Iripin-3, a New Salivary Protein Isolated From Ixodes ricinus Ticks, Displays Immunomodulatory and Anti-Hemostatic Properties In Vitro

Chlastakova, A., Kotal, J., Berankova, Z., Kascakova, B., Martins, L.A., Langhansova, H., Prudnikova, T., Ederova, M., Kotsyfakis, M., Chmelar, J.

(2021) Front Immunol 12: 60

• DOI: https://doi.org/10.3389/fimmu.2021.626200

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 43.24 kDa 
• Atom Count: 3,156 
• Modelled Residue Count: 367 
• Deposited Residue Count: 386 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative salivary serpin	A	355	Ixodes ricinus	Mutation(s): 0
UniProt
Find proteins for A0A0K8RCY5 (Ixodes ricinus) Explore A0A0K8RCY5  Go to UniProtKB:  A0A0K8RCY5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative salivary serpin	B [auth aa]	31	Ixodes ricinus	Mutation(s): 0
UniProt
Find proteins for A0A0K8RCY5 (Ixodes ricinus) Explore A0A0K8RCY5  Go to UniProtKB:  A0A0K8RCY5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
144	C [auth A], D [auth A], E [auth A]	TRIS-HYDROXYMETHYL-METHYL-AMMONIUM C4 H12 N O3 DRDCQJADRSJFFD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.223 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 
• Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.94	α = 90
b = 132.94	β = 90
c = 88.89	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing
XDS	data scaling
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-03-10 
Deposition Author(s): Kascakova, B., Kuta Smatanova, I., Prudnikova, T.

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Funding Organization	Location	Grant Number
Grant Agency of the Czech Republic	Czech Republic	19-14704Y

Revision History  

• Version 1.0: 2021-03-10
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description