1D3V

CRYSTAL STRUCTURE OF THE BINUCLEAR MANGANESE METALLOENZYME ARGINASE COMPLEXED WITH 2(S)-AMINO-6-BORONOHEXANOIC ACID, AN L-ARGININE ANALOG

Structural Biology Knowledgebase: 1D3V SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.179
  • R-Value Work: 0.157

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1D3V

Classification: HYDROLASE

Total Structure Weight: 70642.58

Macromolecule Entities
Molecule Chains Length Organism Details
PROTEIN (ARGINASE) A, B 323 Rattus norvegicus EC#: 3.5.3.1 IUBMB
Gene Name(s): Arg1

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

A, B 2(S)-AMINO-6-BORONOHEXANOIC ACID
C6 H15 B N O5
BLVGFZFOWWBCCZ-YFKPBYRVSA-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 %)
ABH N/A in BindingDB
Kd: 110 nM  BindingMOAD
Kd: 110 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.179
  • R-Value Work: 0.157
  • Space Group: P 3

Unit Cell:

Length (Å) Angle (°)
a = 91.30 α = 90.00
b = 91.30 β = 90.00
c = 69.90 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-10-01
  • Released Date: 1999-11-17
  • Deposition author(s): Cox, J.D., Kim, N.N., Traish, A.M., Christianson, D.W.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4