3LP7 | pdb_00003lp7

Crystal structure of Human Arginase I in complex with inhibitor N(omega)-hydroxy-L-arginine (NOHA), 2.04A Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 
    0.174 (Depositor), 0.174 (DCC) 
  • R-Value Work: 
    0.123 (Depositor), 0.124 (DCC) 
  • R-Value Observed: 
    0.123 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

Inhibition of human arginase I by substrate and product analogues.

Di Costanzo, L.Ilies, M.Thorn, K.J.Christianson, D.W.

(2010) Arch Biochem Biophys 496: 101-108

  • DOI: https://doi.org/10.1016/j.abb.2010.02.004
  • Primary Citation Related Structures: 
    3KV2, 3LP4, 3LP7

  • PubMed Abstract: 

    Human arginase I is a binuclear manganese metalloenzyme that catalyzes the hydrolysis of L-arginine to generate L-ornithine and urea. We demonstrate that N-hydroxy-L-arginine (NOHA) binds to this enzyme with K(d)=3.6 microM, and nor-N-hydroxy-L-arginine (nor-NOHA) binds with K(d)=517 nM (surface plasmon resonance) or K(d) approximately 50 nM (isothermal titration calorimetry). Crystals of human arginase I complexed with NOHA and nor-NOHA afford 2.04 and 1.55 A resolution structures, respectively, which are significantly improved in comparison with previously-determined structures of the corresponding complexes with rat arginase I. Higher resolution structures clarify the binding interactions of the inhibitors. Finally, the crystal structure of the complex with L-lysine (K(d)=13 microM) is reported at 1.90 A resolution. This structure confirms the importance of hydrogen bond interactions with inhibitor alpha-carboxylate and alpha-amino groups as key specificity determinants of amino acid recognition in the arginase active site.


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

Macromolecule Content 

  • Total Structure Weight: 70.16 kDa 
  • Atom Count: 5,064 
  • Modeled Residue Count: 626 
  • 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: 2.04 Å
  • R-Value Free:  0.174 (Depositor), 0.174 (DCC) 
  • R-Value Work:  0.123 (Depositor), 0.124 (DCC) 
  • R-Value Observed: 0.123 (Depositor) 
Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.68α = 90
b = 90.68β = 90
c = 69.82γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description