Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 34.83 kDa 
• Atom Count: 2585 
• Residue Count: 284 
• Unique protein chains: 2

4AG1

Human Chymase - Fynomer Complex

• DOI: 10.2210/pdb4AG1/pdb

• Classification: HYDROLASE/DE NOVO PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-01-23 Released: 2012-07-11 
• Deposition Author(s): Schlatter, D., Brack, S., Banner, D.W., Batey, S., Benz, J., Bertschinger, J., Huber, W., Joseph, C., Rufer, A., Van Der Kloosters, A., Weber, M., Grabulovski, D., Hennig, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.170 
• R-Value Work: 0.139 
• R-Value Observed: 0.140 

Literature

Generation, Characterization and Structural Data of Chymase Binding Proteins Based on the Human Fyn Kinase SH3 Domain.

Schlatter, D., Brack, S., Banner, D.W., Batey, S., Benz, J., Bertschinger, J., Huber, W., Joseph, C., Rufer, A., Van Der Klooster, A., Weber, M., Grabulovski, D., Hennig, M.

(2012) MAbs 4: 497

• PubMed: 22653218 
• DOI: 10.4161/mabs.20452
• Primary Citation of Related Structures:  
  4AFQ, 4AG2, 4AFS, 4AFU, 4AG1, 4AFZ


• PubMed Abstract: 
  

The serine protease chymase (EC = 3.4.21.39) is expressed in the secretory granules of mast cells, which are important in allergic reactions. Fynomers, which are binding proteins derived from the Fyn SH3 domain, were generated against human chymase to produce binding partners to facilitate crystallization, structure determination and structure-based drug discovery, and to provide inhibitors of chymase for therapeutic applications. The best Fynomer was found to bind chymase with a KD of 0.9 nM and koff of 6.6x10 (-4) s (-1) , and to selectively inhibit chymase activity with an IC 50 value of 2 nM. Three different Fynomers were co-crystallized with chymase in 6 different crystal forms overall, with diffraction quality in the range of 2.25 to 1.4 Å resolution, which is suitable for drug design efforts. The X-ray structures show that all Fynomers bind to the active site of chymase. The conserved residues Arg15-Trp16-Thr17 in the RT-loop of the chymase binding Fynomers provide a tight interaction, with Trp16 pointing deep into the S1 pocket of chymase. These results confirm the suitability of Fynomers as research tools to facilitate protein crystallization, as well as for the development of assays to investigate the biological mechanism of targets. Finally, their highly specific inhibitory activity and favorable molecular properties support the use of Fynomers as potential therapeutic agents.

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Organizational Affiliation: 

F. Hoffmann-La Roche Ltd, Pharma Research & Early Development, Discovery Technologies, Basel, Switzerland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHYMASE	A	226	Homo sapiens	Mutation(s): 0  Gene Names: CMA1, CYH, CYM EC: 3.4.21.39
Find proteins for P23946 (Homo sapiens) Explore P23946  Go to UniProtKB:  P23946
NIH Common Fund Data Resources
PHAROS  P23946 GTEx  ENSG00000092009

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FYNOMER	C	84	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.170 
• R-Value Work: 0.139 
• R-Value Observed: 0.140 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.998	α = 90
b = 59.855	β = 90
c = 89.711	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SADABS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-01-23 
• Released Date: 2012-07-11 
Deposition Author(s): Schlatter, D., Brack, S., Banner, D.W., Batey, S., Benz, J., Bertschinger, J., Huber, W., Joseph, C., Rufer, A., Van Der Kloosters, A., Weber, M., Grabulovski, D., Hennig, M.

Revision History 

• Version 1.0: 2012-07-11
  Type: Initial release
  
• Version 1.1: 2012-08-15
  Changes: Database references, Structure summary