1YP9

Trypsin Inhibitor Complex

• PDB DOI: https://doi.org/10.2210/pdb1YP9/pdb

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


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.264 
• R-Value Work: 0.174 
• R-Value Observed: 0.174 

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 of 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: 24.06 kDa 
• Atom Count: 1,824 
• Modelled Residue Count: 223 
• Deposited Residue Count: 223 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cationic trypsin	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UIZ	C [auth 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
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
UIZ	PDBBind:  1YP9	Ki: 7700 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.264 
• R-Value Work: 0.174 
• R-Value Observed: 0.174 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.2	α = 90
b = 63.5	β = 90
c = 69.3	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-23
  Changes: Structure summary