4AOR | pdb_00004aor

Cationic trypsin in complex with the Spinacia oleracea trypsin inhibitor III (SOTI-III)

• PDB DOI: https://doi.org/10.2210/pdb4AOR/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Bos taurus, Spinacia oleracea
• Mutation(s): No 


• Deposited: 2012-03-29 Released: 2013-01-09 
• Deposition Author(s): Schmelz, S., Glotzbach, B., Reinwarth, M., Christmann, A., Kolmar, H., Heinz, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.221 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Structural Characterization of Spinacia Oleracea Trypsin Inhibitor III (Soti-III)

Glotzbach, B., Schmelz, S., Reinwarth, M., Christmann, A., Heinz, D.W., Kolmar, H.

(2013) Acta Crystallogr D Biol Crystallogr 69: 114

• PubMed: 23275169 
• DOI: https://doi.org/10.1107/S0907444912043880
• Primary Citation Related Structures: 
  4AOQ, 4AOR


• PubMed Abstract: 
  

  In recent decades, several canonical serine protease inhibitor families have been classified and characterized. In contrast to most trypsin inhibitors, those from garden four o'clock (Mirabilis jalapa) and spinach (Spinacia oleracea) do not share sequence similarity and have been proposed to form the new Mirabilis serine protease inhibitor family. These 30-40-amino-acid inhibitors possess a defined disulfide-bridge topology and belong to the cystine-knot miniproteins (knottins). To date, no atomic structure of this inhibitor family has been solved. Here, the first structure of S. oleracea trypsin inhibitor III (SOTI-III), in complex with bovine pancreatic trypsin, is reported. The inhibitor was synthesized by solid-phase peptide synthesis on a multi-milligram scale and was assayed to test its inhibitory activity and binding properties. The structure confirmed the proposed cystine-bridge topology. The structural features of SOTI-III suggest that it belongs to a new canonical serine protease inhibitor family with promising properties for use in protein-engineering and medical applications.

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Organizational Affiliation: 
• Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Germany.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 82.96 kDa 
• Atom Count: 6,365 
• Modeled Residue Count: 771 
• Deposited Residue Count: 780 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CATIONIC TRYPSIN	A, B, C	223	Bos taurus	Mutation(s): 0  EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus) Explore P00760  Go to UniProtKB:  P00760

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TRYPSIN INHIBITOR 3	D, E, F	37	Spinacia oleracea	Mutation(s): 0
UniProt
Find proteins for P84781 (Spinacia oleracea) Explore P84781  Go to UniProtKB:  P84781

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	W [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
GOL	G [auth A], H [auth A], I [auth A], J [auth A], P [auth B], X [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	M [auth A], N [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], Y [auth C]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
CA	O [auth A], U [auth B], V [auth B], Z [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	K [auth A], L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.221 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.35	α = 90
b = 66.82	β = 90.17
c = 108.89	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-09 
Deposition Author(s): Schmelz, S., Glotzbach, B., Reinwarth, M., Christmann, A., Kolmar, H., Heinz, D.W.

Revision History  

• Version 1.0: 2013-01-09
  Type: Initial release
  
• Version 1.1: 2013-01-16
  Changes: Database references
• Version 1.2: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary