Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 24073.02 
• Atom Count: 1702 
• Residue Count: 223 
• Unique protein chains: 1

1Y5B

Dianhydrosugar-based benzamidine, factor Xa specific inhibitor in complex with bovine trypsin mutant

• DOI: 10.2210/pdb1Y5B/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Expression System: Escherichia coli
• Mutation(s): 2 


• Deposited: 2004-12-02 Released: 2005-12-13 
• Deposition Author(s): Di Fenza, A., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.221 
• R-Value Work: 0.160 

Literature

Understanding binding selectivity toward trypsin and factor Xa: the role of aromatic interactions

Di Fenza, A., Heine, A., Koert, U., Klebe, G.

(2007) Chemmedchem 2: 297-308

• PubMed: 17191291 
• DOI: 10.1002/cmdc.200600185
• Primary Citation of Related Structures:  
  1Y5U, 1Y5A, 1Y59


• PubMed Abstract: 
  

A congeneric series of four bis-benzamidine inhibitors sharing a dianhydrosugar isosorbide scaffold in common has been studied by crystal structure analysis and enzyme kinetics with respect to their binding to trypsin and factor Xa. Within the series, aromatic interactions are an important determinant for selectivity discrimination among both serine proteases. To study the selectivity-determining features in detail, we used trypsin mutants in which the original binding site is gradually substituted to finally resemble the factor Xa binding pocket. The influence of these mutations has been analyzed on the binding of the closely related inhibitors. We present the crystal structures of the inhibitor complexes obtained by co-crystallizing an "intermediate" trypsin mutant. They could be determined to a resolution of up to 1.2 A, and we measured the inhibitory activity (K(i)) of each ligand against factor Xa, trypsin, and the various mutants. From these data we were able to derive a detailed structure-activity relationship which demonstrates the importance of aromatic interactions in protein-ligand recognition and their role in modulating enzyme selectivity. Pronounced preference is experienced to accommodate the benzamidine anchor with meta topology in the S(1) specificity pocket. One ligand possessing only para topology deviates strongly from the other members of the series and adopts a distinct binding mode addressing the S(1)' site instead of the distal S(3)/S(4) binding pocket.

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Organizational Affiliation: 

Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Trypsin, cationic	T	223	Bos taurus	Mutation(s): 2  EC: 3.4.21.4
Find proteins for P00760 (Bos taurus) Go to UniProtKB:  P00760

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	T	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	T	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
TL3	T	2,5-BIS-O-{4-[AMINO(IMINO)METHYL]PHENYL}-1,4:3,6-DIANHYDRO-D-GLUCITOL 2,5-O,O-BIS-{4',4''-AMIDINOPHENYL}-1,4:3,6-DIANHYDRO-D-SORBITOL C20 H22 N4 O4 CDEVHSIVANGYRI-XMTFNYHQSA-N
IMD	T	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
TL3	Kd: 1260 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.221 
• R-Value Work: 0.160 
• Space Group: P 3₁ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 54.366	α = 90.00
b = 54.366	β = 90.00
c = 105.140	γ = 120.00

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
HKL-2000	data scaling
CrystalClear	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-12-02 
• Released Date: 2005-12-13 
• Deposition Author(s): Di Fenza, A., Heine, A., Klebe, G.

Revision History 

• Version 1.0: 2005-12-13
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-10-11
  Type: Refinement description