1ONW

Crystal structure of Isoaspartyl Dipeptidase from E. coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.178

Literature

Macromolecules
Sequence Display for 1ONW

Classification: HYDROLASE

Total Structure Weight: 82937.01

Macromolecule Entities
Molecule Chains Length Organism Details
Isoaspartyl dipeptidase A, B 390 Escherichia coli EC#: 3.4.19 IUBMB
Mutation: K162X
Gene Name(s): iadA yjiF b4328 JW4291
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
KCX
Query on KCX
A, B L-PEPTIDE LINKING C7 H14 N2 O4 LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.178
  • Space Group: P 4 21 2

Unit Cell:

Length (Å) Angle (°)
a = 116.70 α = 90.00
b = 116.70 β = 90.00
c = 138.50 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-03-02
  • Released Date: 2003-05-06
  • Deposition author(s): Thoden, J.B., Marti-Arbona, R., Raushel, F.M., Holden, H.M.

Revision History

  • Version 1_0: 2003-05-06

    Type: Initial release

  • Version 1_1: 2008-04-29

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Derived calculations, Version format compliance

  • Version 1_3: 2011-11-16

    Type: Atomic model

  • Version 1_4: 2017-10-11

    Type: Refinement description