3GN0

Crystal structure of human arginase I in complex with difluoromethylornithine (DFMO)

Structural Biology Knowledgebase: 3GN0 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.202
  • R-Value Work: 0.161

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3GN0

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 70144.48

Macromolecule Entities
Molecule Chains Length Organism Details
Arginase-1 A, B 322 Homo sapiens EC#: 3.5.3.1 IUBMB
Gene Name(s): ARG1 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DMO
Query on DMO

A, B ALPHA-DIFLUOROMETHYLORNITHINE
C6 H12 F2 N2 O2
VLCYCQAOQCDTCN-ZCFIWIBFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A, B MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DMO N/A in BindingDB
Ki: 3900000 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.202
  • R-Value Work: 0.161
  • Space Group: P 3

Unit Cell:

Length (Å) Angle (°)
a = 89.59 α = 90.00
b = 89.59 β = 90.00
c = 69.02 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-03-15
  • Released Date: 2010-02-23
  • Deposition author(s): Di Costanzo, L., Christianson, D.W.

Revision History

  • 2013-06-19
    Type: Citation | Details: Citation update
  • 2011-07-20
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4