3T62 | pdb_00003t62

Crystal structure of recombinant Kunitz Type serine protease Inhibitor-1 from the Caribbean Sea anemone Stichodactyla helianthus in complex with bovine chymotrypsin

• PDB DOI: https://doi.org/10.2210/pdb3T62/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Bos taurus, Stichodactyla helianthus
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2011-07-28 Released: 2012-08-01 
• Deposition Author(s): Garcia-Fernandez, R., Dominguez, R., Oberthuer, D., Pons, T., Gonzalez-Gonzalez, Y., Chavez, M.A., Betzel, C., Redecke, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.233 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Structural insights into chymotrypsin inhibition by the Kunitz-type inhibitor-1 from the marine invertebrate Stichodactyla helianthus

Garcia-Fernandez, R., Dominguez, R., Oberthuer, D., Pons, T., Gonzalez-Gonzalez, Y., Chavez, M.A., Betzel, C., Redecke, L.

To be published.

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: 95.89 kDa 
• Atom Count: 7,198 
• Modeled Residue Count: 882 
• Deposited Residue Count: 897 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chymotrypsinogen A	A, C [auth B], E [auth C]	245	Bos taurus	Mutation(s): 0  EC: 3.4.21.1
UniProt
Find proteins for P00766 (Bos taurus) Explore P00766  Go to UniProtKB:  P00766

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Kunitz-type proteinase inhibitor SHPI-1	B [auth D], D [auth E], F	54	Stichodactyla helianthus	Mutation(s): 0
UniProt
Find proteins for P31713 (Stichodactyla helianthus) Explore P31713  Go to UniProtKB:  P31713

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A], H [auth A], I [auth B], J [auth B], K [auth E], L [auth E], M [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.233 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 199.706	α = 90
b = 199.706	β = 90
c = 54.572	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
DNA	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-01 
Deposition Author(s): Garcia-Fernandez, R., Dominguez, R., Oberthuer, D., Pons, T., Gonzalez-Gonzalez, Y., Chavez, M.A., Betzel, C., Redecke, L.

Revision History  

• Version 1.0: 2012-08-01
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary