1F57

CARBOXYPEPTIDASE A COMPLEX WITH D-CYSTEINE AT 1.75 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.137 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of carboxypeptidase A complexed with D-cysteine at 1.75 A - inhibitor-induced conformational changes.

van Aalten, D.M.Chong, C.R.Joshua-Tor, L.

(2000) Biochemistry 39: 10082-10089


  • PubMed Abstract: 
  • D-Cysteine differs from the antiarthritis drug D-penicillamine by only two methyl groups on the beta-carbon yet inhibits carboxypeptidase A (CPD) by a distinct mechanism: D-cysteine binds tightly to the active site zinc, while D-penicillamine catalyz ...

    D-Cysteine differs from the antiarthritis drug D-penicillamine by only two methyl groups on the beta-carbon yet inhibits carboxypeptidase A (CPD) by a distinct mechanism: D-cysteine binds tightly to the active site zinc, while D-penicillamine catalyzes metal removal. To investigate the structural basis for this difference, we solved the crystal structure of carboxypeptidase A complexed with D-cysteine (D-Cys) at 1.75-A resolution. D-Cys binds the active site zinc with a sulfur ligand and forms additional interactions with surrounding side chains of the enzyme. The structure explains the difference in potency between D-Cys and L-Cys and provides insight into the mechanism of D-penicillamine inhibition. D-Cys binding induces a concerted motion of the side chains around the zinc ion, similar to that found in other carboxypeptidase-inhibitor crystal structures and along a limited path. Analysis of concerted motions of CPD and CPD-inhibitor crystal structures reveals a clustering of these structures into distinct groups. Using the restricted conformational flexibility of a drug target in this type of analysis could greatly enhance efficiency in drug design.


    Organizational Affiliation

    W. M. Keck Structural Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.




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
DCY
Query on DCY

Download SDF File 
Download CCD File 
A
D-CYSTEINE
C3 H7 N O2 S
XUJNEKJLAYXESH-UWTATZPHSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DCYKi: 2300 nM (99) BINDINGDB
DCYKi: 2300 nM BINDINGMOAD
DCYKi: 2300 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.137 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 44.389α = 90.00
b = 57.712β = 101.62
c = 58.193γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-09-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-31
    Type: Advisory, Experimental preparation