3KER

D-Dopachrome tautomerase (D-DT)/ macrophage migration inhibitory factor 2 (MIF2) complexed with inhibitor 4-IPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution structure of D-DT/MIF2 complexed with 4-IPP

Zierow, S.Lolis, E.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-dopachrome decarboxylase
A, B, C, D
117Mus musculusMutation(s): 0 
Gene Names: Ddt
EC: 4.1.1.84
Find proteins for O35215 (Mus musculus)
Go to UniProtKB:  O35215
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
RW1
Query on RW1

Download SDF File 
Download CCD File 
A, B, C, D
4-phenylpyrimidine
6-phenylpyrimidine
C10 H8 N2
MKLQPIYLZMLAER-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.222 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 82.172α = 90.00
b = 82.172β = 90.00
c = 144.253γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DENZOdata reduction
HKL-2000data scaling
CNSrefinement
SCALEPACKdata scaling
HKL-2000data reduction
PHASERphasing
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-10-26 
  • Released Date: 2010-10-13 
  • Deposition Author(s): Zierow, S., Lolis, E.

Revision History 

  • Version 1.0: 2010-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description