1AFQ

CRYSTAL STRUCTURE OF BOVINE GAMMA-CHYMOTRYPSIN COMPLEXED WITH A SYNTHETIC INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

X-ray crystal structure of a dipeptide-chymotrypsin complex in an inhibitory interaction.

Kashima, A.Inoue, Y.Sugio, S.Maeda, I.Nose, T.Shimohigashi, Y.

(1998) Eur J Biochem 255: 12-23

  • DOI: https://doi.org/10.1046/j.1432-1327.1998.2550012.x
  • Primary Citation of Related Structures:  
    1AB9, 1AFQ

  • PubMed Abstract: 

    The dipeptide D-leucyl-L-phenylalanyl p-fluorobenzylamide (D-Leu-Phe-NH-BzlF) inhibits chymotrypsin strongly in a competitive manner with the Ki value of 0.61 microM [Shimohigashi, Y., Maeda, I., Nose, T., Ikesue, K., Sakamoto, H., Ogawa, T., Ide, Y., Kawahara, M., Nezu, T., Terada, Y., Kawano, K. & Ohno, M. (1996) J. Chem. Soc. Perkin Trans. 1, 2479-2485]. The structure/activity studies have suggested a unique inhibitory conformation, in which the C-terminal benzyl group fits the chymotrypsin S1 site and the hydrophobic core constructed by the side chains of D-Leu-Phe fits the S2 or S1' site. To verify this assumption, the molecular structure of the complex between the dipeptide and gamma-chymotrypsin has been determined crystallographically. Gamma-chymotrypsin itself was first crystallized and refined at 1.6-A resolution. The refined structure was virtually identical to the conformation reported and the electron density at the active site was interpreted as a pentapeptide Thr-Pro-Gly-Val-Tyr derived from autolysis of the enzyme (residues 224-228). The chymotrypsin-dipeptide complex was obtained by soaking the crystals of gamma-chymotrypsin in a solution saturated with the dipeptide inhibitor. The crystal structure of the complex has been refined at 1.8-A resolution to a crystallographic R-factor of 18.1%. The structure of gamma-chymotrypsin in the complex agreed fairly well with that of gamma-chymotrypsin per se with a rmsd of 0.13 A for all the C alpha carbons. Two inhibitor molecules were assigned in an asymmetric unit, i.e. one in the active site and the other at the interface of two symmetry-related enzyme molecules. In both sites dipeptides adopted very similar folded conformations, in which side chains of D-Leu-Phe are spatially proximal. In the active site where the binding of dipeptide was judged to be a direct cause of inhibition, C-terminal p-fluorobenzylamide group of the dipeptide, NH-BzlF, was found in the S1 hydrophobic pocket. At the bottom of this pocket, the p-fluorine atom hydrogen bonded with a water molecule, probably to enhance the inhibitory activity. The stereospecific interaction of R and S isomers of the dipeptide with C-terminal NH-C*H(CH3)-C6H5 was well explained by the space available for methyl replacement in the complex. The hydrophobic core constructed by side chains of D-Leu-Phe was found at the broad S2 site. Interestingly, a novel interaction was found between the inhibitor Phe residue and chymotrypsin His57, the phenyl of Phe and the imidazole of His being in a pi-pi stacking interaction at a distance 3.75 A.


  • Organizational Affiliation

    Research Division, The Green Cross Corp., Hirakata, Japan.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BOVINE GAMMA-CHYMOTRYPSIN13Bos taurusMutation(s): 0 
EC: 3.4.21.1
UniProt
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Go to UniProtKB:  P00766
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00766
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BOVINE GAMMA-CHYMOTRYPSIN131Bos taurusMutation(s): 0 
EC: 3.4.21.1
UniProt
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Go to UniProtKB:  P00766
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
BOVINE GAMMA-CHYMOTRYPSIN96Bos taurusMutation(s): 0 
EC: 3.4.21.1
UniProt
Find proteins for P00766 (Bos taurus)
Explore P00766 
Go to UniProtKB:  P00766
Entity Groups  
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UniProt GroupP00766
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  • Reference Sequence
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.84α = 90
b = 69.84β = 90
c = 97.36γ = 90
Software Package:
Software NamePurpose
CONTROLdata collection
PROCESSdata reduction
X-PLORmodel building
X-PLORrefinement
CONTROLdata reduction
PROCESSdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 0FGClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-09-17
    Type: Initial release
  • Version 1.1: 2008-03-04
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 1.4: 2023-08-02
    Changes: Database references, Derived calculations, Other, Refinement description
  • Version 1.5: 2024-10-30
    Changes: Data collection, Structure summary