4HZE

Crystal structure of human Arginase-2 complexed with inhibitor 9

Structural Biology Knowledgebase: 4HZE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.198
  • R-Value Work: 0.174

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4HZE

Classification: Hydrolase / Hydrolase Inhibitor

Total Structure Weight: 101764.11

Macromolecule Entities
Molecule Chains Length Organism Details
Arginase-2, mitochondrial A, B, C 306 Homo sapiens EC#: 3.5.3.1 IUBMB
Gene Name(s): ARG2 Gene View

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
X7A
Query on X7A

A, B, C [(5R)-5-amino-5-carboxy-7-(piperidin-1-yl)heptyl](trihydroxy)borate(1- )
C13 H28 B N2 O5
SCRPJEVETAWLOZ-CYBMUJFWSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BEN
Query on BEN

A, B, C BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BME
Query on BME

A, B, C BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A, B, C MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
X7A N/A in BindingDB
IC50: 1920 nM  BindingMOAD
IC50: 509 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.198
  • R-Value Work: 0.174
  • Space Group: P 42 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 127.74 α = 90.00
b = 127.74 β = 90.00
c = 159.11 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-11-15
  • Released Date: 2013-03-20
  • Deposition author(s): Cousido-Siah, A., Mitschler, A., Ruiz, F.X., Whitehouse, D.L., Golebiowski, A., Ji, M., Zhang, M., Beckett , P., Sheeler, R., Andreoli, M., Conway, B., Mahboubi, K., Schroeter, H., Van Zandt, M.C., Podjarny, A.

Revision History

  • 2013-04-10
    Type: Citation | Details: Citation update