1CBX

CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN CARBOXYPEPTIDASE A AND THE BIPRODUCT ANALOG INHIBITOR L-BENZYLSUCCINATE AT 2.0 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the complex between carboxypeptidase A and the biproduct analog inhibitor L-benzylsuccinate at 2.0 A resolution.

Mangani, S.Carloni, P.Orioli, P.

(1992) J.Mol.Biol. 223: 573-578


  • PubMed Abstract: 
  • The X-ray crystal structure of the carboxypeptidase A-L-benzylsuccinate complex has been refined at 2.0 A resolution to a final R-factor of 0.166. One molecule of the inhibitor binds to the enzyme active site. The terminal carboxylate forms a salt li ...

    The X-ray crystal structure of the carboxypeptidase A-L-benzylsuccinate complex has been refined at 2.0 A resolution to a final R-factor of 0.166. One molecule of the inhibitor binds to the enzyme active site. The terminal carboxylate forms a salt link with the guanidinium group of Arg145 and hydrogen bonds with Tyr248 and Asn144. The second carboxylate group binds to the zinc ion in an asymmetric bidentate fashion replacing the water molecule of the native structure. The zinc ion moves 0.5 A from its position in the native structure to accommodate the inhibitor binding. The overall stereochemistry around the zinc can be considered a distorted tetrahedron, although six atoms of the co-ordinated groups lie within 3.0 A from the zinc ion. The key for the strong inhibitory properties of L-benzylsuccinate can be found in its ability both to co-ordinate the zinc and to form a short carboxyl-carboxylate-type hydrogen bond (2.5 A) with Glu270.


    Related Citations: 
    • Refined Crystal Structure of Carboxypeptidase a at 1.54 Angstroms Resolution
      Rees, D.C.,Lewis, M.,Lipscomb, W.N.
      (1983) J.Mol.Biol. 168: 367


    Organizational Affiliation

    Dipartimento di Chimica, Università di Siena, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CARBOXYPEPTIDASE A
A
307Bos taurusGene Names: CPA1 (CPA)
EC: 3.4.17.1
Find proteins for P00730 (Bos taurus)
Go to Gene View: CPA1
Go to UniProtKB:  P00730
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
BZS
Query on BZS

Download SDF File 
Download CCD File 
A
L-BENZYLSUCCINIC ACID
C11 H12 O4
GTOFKXZQQDSVFH-SECBINFHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BZSKi: 450 nM BINDINGMOAD
BZSKi: 450 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.600α = 90.00
b = 60.270β = 97.27
c = 47.250γ = 90.00
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other