3FVL | pdb_00003fvl

Crystallogic studies on the Complex of Carboxypeptidase A with inhibitors using alpha-hydroxy ketone as zinc-binding group

• PDB DOI: https://doi.org/10.2210/pdb3FVL/pdb

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


• Deposited: 2009-01-16 Released: 2010-01-12 
• Deposition Author(s): Wang, S.F., Jin, J.-Y., Tian, G.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.238 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Optical 2-benzyl-5-hydroxy4oxopentanoic acids against carboxypeptidase A: Synthesis, kinetic evaluation and X-ray crystallographic study

Wang, S.F., Jin, J.-Y., Zeng, Z.H., Tian, G.R.

(2010) Chin Chem Lett 21: 159-162

• DOI: https://doi.org/10.1016/j.cclet.2009.09.005

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 104.37 kDa 
• Atom Count: 7,907 
• Modeled Residue Count: 921 
• Deposited Residue Count: 921 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carboxypeptidase A1	A, B [auth C], C [auth E]	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
BHK	E [auth A], G [auth C], I [auth E]	(2R)-2-benzyl-5-hydroxy-4-oxopentanoic acid C12 H14 O4 HHXVRTWUQBYAFG-SNVBAGLBSA-N
ZN	D [auth A], F [auth C], H [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.238 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.347	α = 90
b = 59.786	β = 103.94
c = 99.36	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNS	refinement
HKL-2000	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-12 
Deposition Author(s): Wang, S.F., Jin, J.-Y., Tian, G.R.

Revision History  

• Version 1.0: 2010-01-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary