1YME

STRUCTURE OF CARBOXYPEPTIDASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Work: 0.148 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Carboxypeptidase A: native, zinc-removed and mercury-replaced forms.

Greenblatt, H.M.Feinberg, H.Tucker, P.A.Shoham, G.

(1998) Acta Crystallogr D Biol Crystallogr 54: 289-305

  • DOI: 10.1107/s0907444997010445
  • Primary Citation of Related Structures:  
    1YME, 1ARM, 1ARL

  • PubMed Abstract: 
  • The crystal structure of the zinc-containing exopeptidase bovine carboxypeptidase A (CPA) has been refined to high resolution, based on a data set collected from a single crystal, incorporating new sequence information based on cloning of the bovine gene ...

    The crystal structure of the zinc-containing exopeptidase bovine carboxypeptidase A (CPA) has been refined to high resolution, based on a data set collected from a single crystal, incorporating new sequence information based on cloning of the bovine gene. In addition, new refined structures are available for the zinc-removed form of the enzyme, apo-CPA, as well as the mercury-replaced form, Hg-CPA. The native structure reveals that the zinc-bound water molecule does not appear to more loosely bound than the rest of the zinc ligands, at least when B-factor values are considered. Nor is there any evidence for a secondary location of this water molecule. The apo-enzyme structure does not show any density in the place of the removed zinc ion. The only significant change appears to be a chi2 rotation of one zinc histidine ligand to form an ion-pair interaction with a glutamic acid side chain. The structure of Hg-CPA reveals a solvent Tris molecule bound to the mercury cation, as well as an unidentified cation bound to Glu270. The location of this citation agrees with previous proposals for the binding side of inhibitory zinc. These observations may explain some of the differences in kinetics observed in metal- replaced CPA.


    Organizational Affiliation

    Department of Inorganic and Analytical Chemistry, Hebrew University, Jerusalem, Israel, 91904.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CARBOXYPEPTIDASE A ALPHAA309Bos taurusMutation(s): 0 
Gene Names: CPA1CPA
EC: 3.4.17.1
UniProt
Find proteins for P00730 (Bos taurus)
Explore P00730 
Go to UniProtKB:  P00730
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Work: 0.148 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.62α = 90
b = 60.17β = 97.4
c = 47.17γ = 90
Software Package:
Software NamePurpose
RIGAKUdata collection
PROLSQrefinement
TNTrefinement
RIGAKUdata reduction

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-02-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance