3FX6 | pdb_00003fx6

X-RAY crystallographic studies on the complex of carboxypeptidase A with the inhibitor using alpha-nitro ketone as the zinc-binding group

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.239 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
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Literature

Characterization of alpha-nitromethyl ketone as a new zinc-binding group based on structural analysis of its complex with carboxypeptidase A

Wang, S.F., Tian, G.R., Zhang, W.Z., Jin, J.Y.

(2009) Bioorg Med Chem Lett 19: 5009-5011

  • DOI: https://doi.org/10.1016/j.bmcl.2009.07.060
  • Primary Citation Related Structures: 
    3FX6

  • PubMed Abstract: 

    Zinc-binding groups (ZBGs) are exhaustively applied in the development of the new inhibitors against a wide variety of physiologically and pathologically important zinc proteases. Here the alpha-nitro ketone was presented as a new ZBG, which is a transition-state analog featured by the unique bifurcated hydrogen bonds at the active site of carboxypeptidase A based on the structural analysis. Introduction of a nitro group at the alpha-position of the ketone could provide more non-covalent interactions without loss of the abilities to form a tetrahedral transition-state analog.

    • Organizational Affiliation: 
    • Key Laboratory of Biological Resources and Functional Molecules of the Changbai Mountains, Ministry of Education, Yanbian University, Yanji, Jilin, China.

Macromolecule Content 

  • Total Structure Weight: 104.51 kDa 
  • Atom Count: 7,924 
  • Modeled Residue Count: 921 
  • Deposited Residue Count: 921 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Carboxypeptidase A1A,
B [auth C],
C [auth E]		307Bos taurusMutation(s): 0 
EC: 3.4.17.1
UniProt
Find proteins for P00730 (Bos taurus)
Explore P00730 
Go to UniProtKB:  P00730
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00730
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.239 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.356α = 90
b = 59.752β = 104.04
c = 99.514γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
CNSrefinement
HKL-2000data reduction
SCALAdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary