3KER | pdb_00003ker

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 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.222 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Targeting distinct tautomerase sites of D-DT and MIF with a single molecule for inhibition of neutrophil lung recruitment.

Rajasekaran, D.Zierow, S.Syed, M.Bucala, R.Bhandari, V.Lolis, E.J.

(2014) FASEB J 28: 4961-4971

  • DOI: https://doi.org/10.1096/fj.14-256636
  • Primary Citation Related Structures: 
    3KAN, 3KER, 4Q3F

  • PubMed Abstract: 

    We report a new inflammatory activity for extracellular d-dopachrome tautomerase (D-DT), the recruitment of neutrophils to the lung on D-DT intratracheal installation of C57BL/6J mice with an EC50 of 5.6 μg. We also find that D-DT and macrophage migration inhibitory factor (MIF) have additive effects in neutrophil recruitment. Although the tautomerase site of D-DT and its homologue MIF are biophysically very different, 4-iodo-6-phenylpyrimidine (4-IPP) forms a covalent bond with Pro-1 of both proteins, resulting in a 6-phenylpyrimidine (6-PP) adduct. Recruitment of neutrophils to the lung for the 6-PP adducts of D-DT and MIF are reduced by ∼ 50% relative to the apo proteins, demonstrating that an unmodified Pro-1 is important for this activity, but there is no cooperativity in inhibition of the proteins together. The differences in the binding mode of the 6-PP adduct for D-DT was determined by crystallographic studies at 1.13 Å resolution and compared to the structure of the MIF-6-PP complex. There are major differences in the location of the 6-PP adduct to the D-DT and MIF active sites that provide insight into the lack of cooperativity by 4-IPP and into tuning the properties of the covalent inhibitors of D-DT and MIF that are necessary for the development of therapeutic small molecules against neutrophil damage from lung infections such as Pseudomonas aeruginosa in cystic fibrosis and immunocompromised patients.


  • Organizational Affiliation
    • Department of Pharmacology.

Macromolecule Content 

  • Total Structure Weight: 52.98 kDa 
  • Atom Count: 3,704 
  • Modeled Residue Count: 468 
  • Deposited Residue Count: 468 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
D-dopachrome decarboxylase
A, B, C, D
117Mus musculusMutation(s): 0 
Gene Names: Ddt
EC: 4.1.1.84
UniProt
Find proteins for O35215 (Mus musculus)
Explore O35215 
Go to UniProtKB:  O35215
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO35215
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RW1

Query on RW1



Download:Ideal Coordinates CCD File
E [auth A],
J [auth B],
O [auth C],
T [auth D]
4-phenylpyrimidine
C10 H8 N2
MKLQPIYLZMLAER-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
I [auth A]
K [auth B]
L [auth B]
F [auth A],
G [auth A],
I [auth A],
K [auth B],
L [auth B],
N [auth B],
P [auth C],
Q [auth C],
S [auth C],
U [auth D],
V [auth D],
X [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
H [auth A],
M [auth B],
R [auth C],
W [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free:  0.238 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.222 (DCC) 
Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.172α = 90
b = 82.172β = 90
c = 144.253γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2020-10-21
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2024-11-27
    Changes: Structure summary