3KGQ | pdb_00003kgq

Carboxypeptidase A liganded to an organic small-molecule: conformational changes

• PDB DOI: https://doi.org/10.2210/pdb3KGQ/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2009-10-29 Released: 2010-10-27 
• Deposition Author(s): Fernandez, D., Boix, E., Pallares, I., Aviles, F.X., Vendrell, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.204 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Structural and Functional Analysis of the Complex between Citrate and the Zinc Peptidase Carboxypeptidase A

Fernandez, D., Boix, E., Pallares, I., Aviles, F.X., Vendrell, J.

(2011) Enzyme Res 2011: 128676-128676

• PubMed: 21804935 
• DOI: https://doi.org/10.4061/2011/128676
• Primary Citation Related Structures: 
  3KGQ


• PubMed Abstract: 
  

  A high-resolution carboxypeptidase-Zn(2+)-citrate complex was studied by X-ray diffraction and enzyme kinetics for the first time. The citrate molecule acts as a competitive inhibitor of this benchmark zinc-dependent peptidase, chelating the catalytic zinc ion in the active site of the enzyme and inducing a conformational change such that carboxypeptidase adopts the conformation expected to occur by substrate binding. Citrate adopts an extended conformation with half of the molecule facing the zinc ion, while the other half is docked in the S1' hydrophobic specificity pocket of the enzyme, in contrast with the binding mode expected for a substrate like phenylalanine or a peptidomimetic inhibitor like benzylsuccinic acid. Combined structural and enzymatic analysis describes the characteristics of the binding of this ligand that, acting against physiologically relevant zinc-dependent proteases, may serve as a general model in the design of new drug-protecting molecules for the oral delivery of drugs of peptide origin.

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Organizational Affiliation: 
• Departament de Bioquímica i Biologia Molecular, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.82 kDa 
• Atom Count: 2,691 
• Modeled Residue Count: 303 
• Deposited Residue Count: 309 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carboxypeptidase A1	A	309	Bos taurus	Mutation(s): 0  EC: 3.4.17.1
UniProt
Find proteins for P00730 (Bos taurus) Explore P00730  Go to UniProtKB:  P00730

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	D [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
GOL	I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACN	E [auth A]	ACETONE C3 H6 O CSCPPACGZOOCGX-UHFFFAOYSA-N
FMT	F [auth A], G [auth A], H [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.204 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.604	α = 90
b = 57.006	β = 102.04
c = 60.604	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
AUTOMAR	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-27 
Deposition Author(s): Fernandez, D., Boix, E., Pallares, I., Aviles, F.X., Vendrell, J.

Revision History  

• Version 1.0: 2010-10-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-08-03
  Changes: Database references
• Version 1.3: 2013-06-12
  Changes: Database references
• Version 1.4: 2017-10-04
  Changes: Advisory, Data collection
• Version 1.5: 2023-11-01
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
• Version 1.6: 2024-11-13
  Changes: Structure summary