4FCK | pdb_00004fck

Crystal Structure of the Co2+2-Human Arginase I-AGPA Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.307 (Depositor), 0.305 (DCC) 
  • R-Value Work: 
    0.273 (Depositor), 0.273 (DCC) 
  • R-Value Observed: 
    0.273 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history

Literature

Binding of the unreactive substrate analog L-2-amino-3-guanidinopropionic acid (dinor-L-arginine) to human arginase I.

D'Antonio, E.L.Christianson, D.W.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 889-893

  • DOI: https://doi.org/10.1107/S1744309112027820
  • Primary Citation Related Structures: 
    4FCI, 4FCK

  • PubMed Abstract: 

    Human arginase I (HAI) is a binuclear manganese metalloenzyme that catalyzes the hydrolysis of L-arginine to form L-ornithine and urea through a metal-activated hydroxide mechanism. Since HAI regulates L-Arg bioavailability for NO biosynthesis, it is a potential drug target for the treatment of cardiovascular diseases such as atherosclerosis. X-ray crystal structures are now reported of the complexes of Mn(2)(2+)-HAI and Co(2)(2+)-HAI with L-2-amino-3-guanidinopropionic acid (AGPA; also known as dinor-L-arginine), an amino acid bearing a guanidinium side chain two methylene groups shorter than that of L-arginine. Hydrogen bonds to the α-carboxylate and α-amino groups of AGPA dominate enzyme-inhibitor recognition; the guanidinium group does not interact directly with the metal ions.


  • Organizational Affiliation
    • Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA.

Macromolecule Content 

  • Total Structure Weight: 70.09 kDa 
  • Atom Count: 5,040 
  • Modeled Residue Count: 628 
  • Deposited Residue Count: 644 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Arginase-1
A, B
322Homo sapiensMutation(s): 0 
Gene Names: ARG1
EC: 3.5.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for P05089 (Homo sapiens)
Explore P05089 
Go to UniProtKB:  P05089
PHAROS:  P05089
GTEx:  ENSG00000118520 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05089
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.307 (Depositor), 0.305 (DCC) 
  • R-Value Work:  0.273 (Depositor), 0.273 (DCC) 
  • R-Value Observed: 0.273 (Depositor) 
Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.451α = 90
b = 90.451β = 90
c = 69.362γ = 120
Software Package:
Software NamePurpose
CBASSdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-20
    Type: Initial release
  • Version 1.1: 2012-08-15
    Changes: Database references
  • Version 1.2: 2013-01-23
    Changes: Database references
  • Version 1.3: 2018-12-05
    Changes: Data collection, Experimental preparation, Refinement description, Source and taxonomy
  • Version 1.4: 2019-11-20
    Changes: Derived calculations
  • Version 1.5: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description