1CBX | pdb_00001cbx

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

• PDB DOI: https://doi.org/10.2210/pdb1CBX/pdb

• Classification: HYDROLASE(C-TERMINAL PEPTIDASE)
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 1991-10-31 Released: 1994-01-31 
• Deposition Author(s): Mangani, S., Carloni, P., Orioli, P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Observed: 
  0.166 (Depositor) 

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 Biology 223: 573-578

• PubMed: 1738164 
• DOI: https://doi.org/10.1016/0022-2836(92)90671-6
• Primary Citation Related Structures: 
  1CBX


• 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 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.

---

Organizational Affiliation: 
• Dipartimento di Chimica, Università di Siena, Italy.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.72 kDa 
• Atom Count: 2,631 
• Modeled Residue Count: 307 
• Deposited Residue Count: 307 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CARBOXYPEPTIDASE A	A	307	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BZS	C [auth A]	L-BENZYLSUCCINIC ACID C11 H12 O4 GTOFKXZQQDSVFH-SECBINFHSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.6	α = 90
b = 60.27	β = 97.27
c = 47.25	γ = 90

Software Package:

Software Name	Purpose
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-01-31 
Deposition Author(s): Mangani, S., Carloni, P., Orioli, P.

Revision History  

• Version 1.0: 1994-01-31
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary