4F2K

Macrophage Migration Inhibitory Factor covalently complexed with phenethylisothiocyanate

• PDB DOI: https://doi.org/10.2210/pdb4F2K/pdb

• Classification: ISOMERASE/ISOMERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-05-08 Released: 2012-06-06 
• Deposition Author(s): Tyndall, J.D.A., Bernhagen, J., Hampton, M.B., Wilbanks, S.M., Rutledge, M.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.228 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 

Literature

Macrophage migration inhibitory factor covalently complexed with phenethyl isothiocyanate

Tyndall, J.D.A., Lue, H., Rutledge, M.T., Bernhagen, J., Hampton, M.B., Wilbanks, S.M.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 999-1002

• PubMed: 22949182 
• DOI: https://doi.org/10.1107/S1744309112030552
• Primary Citation of Related Structures:  
  4F2K


• PubMed Abstract: 
  

  Macrophage migration inhibitory factor is irreversibly inhibited via covalent modification by phenethyl isothiocyanate, a naturally occurring compound with anti-inflammatory and anticancer properties. The structure of the modified protein obtained from X-ray diffraction data to 1.64 Å resolution is presented. The inhibitor sits within a deep hydrophobic pocket between subunits of the homotrimer and is highly ordered. The secondary structure of macrophage migratory inhibitory factor is unchanged by this modification, but there are significant rearrangements, including of the side-chain position of Tyr37 and the main chain of residues 31-34. These changes may explain the decreased binding of the modified protein to the receptor CD74. Together with the pocket, the areas of conformational change define specific targets for the design of more selective and potent inhibitors as potential therapeutics.

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Organizational Affiliation: 

School of Pharmacy, University of Otago, PO Box 56, Dunedin 9054, New Zealand.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 38.19 kDa 
• Atom Count: 3,081 
• Modelled Residue Count: 342 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage migration inhibitory factor	A, B, C	114	Homo sapiens	Mutation(s): 0  Gene Names: GLIF, MIF, MMIF EC: 5.3.2.1 (PDB Primary Data), 5.3.3.12 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P14174 (Homo sapiens) Explore P14174  Go to UniProtKB:  P14174
PHAROS:  P14174 GTEx:  ENSG00000240972

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LE2	D [auth A], G [auth B], K [auth C]	N-(2-phenylethyl)thioformamide C9 H11 N S WVJCPUDEWCGDGL-UHFFFAOYSA-N
SO4	E [auth A], H [auth B], L [auth C], M [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
IPA	F [auth A], I [auth B], J [auth B], N [auth C]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.228 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.728	α = 90
b = 68.245	β = 90
c = 88.715	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-06 
Deposition Author(s): Tyndall, J.D.A., Bernhagen, J., Hampton, M.B., Wilbanks, S.M., Rutledge, M.T.

Revision History  

• Version 1.0: 2012-06-06
  Type: Initial release
  
• Version 1.1: 2012-12-26
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description