1Y3Y | pdb_00001y3y

TRYPSIN INHIBITOR COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1Y3Y/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2004-11-26 Released: 2005-12-06 
• Deposition Author(s): Fokkens, J., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.199 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

A simple protocol to estimate differences in protein binding affinity for enantiomers without prior resolution of racemates.

Fokkens, J., Klebe, G.

(2006) Angew Chem Int Ed Engl 45: 985-989

• PubMed: 16374786 
• DOI: https://doi.org/10.1002/anie.200502302
• Primary Citation Related Structures: 
  1Y3V, 1Y3W, 1Y3X, 1Y3Y, 1YP9, 1YPE, 1YPG, 1YPJ, 1YPK

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Organizational Affiliation: 
• Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 23.82 kDa 
• Atom Count: 1,805 
• Modeled Residue Count: 223 
• Deposited Residue Count: 223 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UIR	C [auth A]	(1R,3AS,4R,8AS,8BR)-4-(2-BENZO[1,3]DIOXOL-5-YL-1-CYCLOPROPYL-3-OXO-DECAHYDRO-PYRROLO[3,4-A]PYRROLIZIN-4-YL)-BENZAMIDINE C27 H30 N4 O3 XYMBMAVAMICSMV-FTSNLURZSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.199 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.852	α = 90
b = 54.852	β = 90
c = 109.166	γ = 120

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-06 
Deposition Author(s): Fokkens, J., Klebe, G.

Revision History  

• Version 1.0: 2005-12-06
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-11-13
  Changes: Structure summary