Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 24057.16 
• Atom Count: 1678 
• Residue Count: 223 
• Unique protein chains: 1

1YP9

Trypsin Inhibitor Complex

• DOI: 10.2210/pdb1YP9/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus


• Deposited: 2005-01-31 Released: 2006-01-17 
• Deposition Author(s): Fokkens, J., Obst-Sander, U., Heine, A., Diederich, F., Klebe, G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.264 
• R-Value Work: 0.174 

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: 10.1002/anie.200502302
• Primary Citation of Related Structures:  
  1YPK, 1YPJ, 1YPG, 1YPE, 1Y3Y, 1Y3X, 1Y3W, 1Y3V

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cationic trypsin	A	223	Bos taurus	Mutation(s): 0  EC: 3.4.21.4
Find proteins for P00760 (Bos taurus) Go to UniProtKB:  P00760

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
UIZ	A	(1R,3AS,4R,8AS,8BR)-4-(2-BENZO[1,3]DIOXOL-5-YLMETHYL)-1-BENZYL-3-OXO-DECAHYDRO-PYRROLO[3,4-A]PYRROZILIN-4-YL-BENZAMIDINE C31 H32 N4 O3 APELQVQIJUTSME-UDOPOUDQSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
UIZ	Ki: 7700 nM BINDINGMOAD
UIZ	Ki: 7700 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.264 
• R-Value Work: 0.174 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 61.200	α = 90.00
b = 63.500	β = 90.00
c = 69.300	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-01-31 
• Released Date: 2006-01-17 
• Deposition Author(s): Fokkens, J., Obst-Sander, U., Heine, A., Diederich, F., Klebe, G.

Revision History 

• Version 1.0: 2006-01-17
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-11
  Type: Refinement description