5CPA

REFINED CRYSTAL STRUCTURE OF CARBOXYPEPTIDASE A AT 1.54 ANGSTROMS RESOLUTION.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Refined crystal structure of carboxypeptidase A at 1.54 A resolution.

Rees, D.C.Lewis, M.Lipscomb, W.N.

(1983) J Mol Biol 168: 367-387

  • DOI: 10.1016/s0022-2836(83)80024-2
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The crystal structure of bovine carboxypeptidase A (Cox) has been refined at 1.54 A resolution using the restrained least-squares algorithm of Hendrickson & Konnert (1981). The crystallographic R factor (formula; see text) for structure factors calcu ...

    The crystal structure of bovine carboxypeptidase A (Cox) has been refined at 1.54 A resolution using the restrained least-squares algorithm of Hendrickson & Konnert (1981). The crystallographic R factor (formula; see text) for structure factors calculated from the final model is 0.190. Bond lengths and bond angles in the carboxypeptidase A model have root-mean-square deviations from ideal values of 0.025 A and 3.6 degrees, respectively. Four examples of a reverse turn like structure (the "Asx" turn) requiring an aspartic acid or asparagine residue are observed in this structure. The Asx turn has the same number of atoms as a reverse turn, but only one peptide bond, and the hydrogen bond that closes the turn is between the Asx side-chain CO group and a main-chain NH group. The distributions of CO-N and NH-O hydrogen bond angles in the alpha-helices and beta-sheet structures of carboxypeptidase A are centered about 156 degrees. A total of 192 water molecules per molecule of enzyme are included in the final model. Unlike the hydrogen bonding geometry observed in the secondary structure of the enzyme, the CO-O(wat) hydrogen bond angle is distributed about 131 degrees, indicating the role of the lone pair electrons of the carbonyl oxygen in the hydrogen bond interaction. Twenty four solvent molecules are observed buried within the protein. Several of these waters are organized into hydrogen-bonded chains containing up to five waters. The average temperature factor for atoms in carboxypeptidase A is 8 A2, and varies from 5 A2 in the center of the protein, to over 30 A2 at the surface.


    Related Citations: 
    • Crystallographic Studies on Apocarboxypeptidase a and the Complex with Glycyl-L-Tyrosine
      Rees, D.C., Lipscomb, W.N.
      (1983) Proc Natl Acad Sci U S A 80: 7151
    • Binding of Ligands to the Active Site of Carboxypeptidase A
      Rees, D.C., Lipscomb, W.N.
      (1981) Proc Natl Acad Sci U S A 78: 5455
    • Zinc Environment and Cis Peptide Bonds in Carboxypeptidase a at 1.75-Angstroms Resolution
      Rees, D.C., Lewis, M., Honzatko, R.B., Lipscomb, W.N., Hardman, K.D.
      (1981) Proc Natl Acad Sci U S A 78: 3408
    • Carboxypeptidase a Mechanisms
      Lipscomb, W.N.
      (1980) Proc Natl Acad Sci U S A 77: 3875
    • Carboxypeptidase A,A Protein and an Enzyme
      Quiocho, F.A., Lipscomb, W.N.
      (1971) Adv Protein Chem 25: 1
    • Structure and Mechanism in the Enzymatic Activity of Carboxypeptidase a and Relations to Chemical Sequence
      Lipscomb, W.N.
      (1970) Acc Chem Res 3: 81
    • The Structure of Carboxypeptidase A, Vii.The 2.0-Angstroms Resolution Studies of the Enzyme and of its Complex with Glycyltyrosine,and Mechanistic Deductions
      Lipscomb, W.N., Hartsuck, J.A., Reekejunior, G.N., Quiocho, F.A., Bethge, P.H., Ludwig, M.L., Steitz, T.A., Muirhead, H., Coppola, J.C.
      (1969) Brookhaven Symposia In Biology 21: 24

    Organizational Affiliation

    Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CARBOXYPEPTIDASE A
A
307Bos taurusMutation(s): 0 
Gene Names: CPA1CPA
EC: 3.4.17.1
Find proteins for P00730 (Bos taurus)
Go to UniProtKB:  P00730
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.6α = 90
b = 60.27β = 97.27
c = 47.25γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1982-05-06 
  • Released Date: 1982-07-29 
  • Deposition Author(s): Lipscomb, W.N.

Revision History 

  • Version 1.0: 1982-07-29
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other