5XEJ

Crystal Structure of Macrophage Migration Inhibitory Factor bound to MTX

• PDB DOI: https://doi.org/10.2210/pdb5XEJ/pdb
• Entry: 5XEJ supersedes: 5CG4

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


• Deposited: 2017-04-05 Released: 2018-07-25 
• Deposition Author(s): Takimoto-Kamimura, M., Fukushima, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.227 
• R-Value Work: 0.180 
• R-Value Observed: 0.183 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 5CG4

Literature

Structure of macrophage migration inhibitory factor in complex with methotrexate.

Fukushima, K., Furuya, M., Kamimura, T., Takimoto-Kamimura, M.

(2021) Acta Crystallogr D Struct Biol 77: 293-299

• PubMed: 33645533 
• DOI: https://doi.org/10.1107/S2059798321000474
• Primary Citation of Related Structures:  
  5XEJ


• PubMed Abstract: 
  

  Methotrexate (MTX) is an anticancer and anti-rheumatoid arthritis drug that is considered to block nucleotide synthesis and the cell cycle mainly by inhibiting the activity of dihydrofolate reductase (DHFR). Using affinity-matrix technology and X-ray analysis, the present study shows that MTX also interacts with macrophage migration inhibitory factor (MIF). Fragment molecular-orbital calculations quantified the interaction between MTX and MIF based on the structure of the complex and revealed the amino acids that are effective in the interaction of MTX and MIF. It should be possible to design new small-molecule compounds that have strong inhibitory activity towards both MIF and DHFR by structure-based drug discovery.

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Organizational Affiliation: 

Pharmaceutical Discovery Research Laboratories, Teijin Institute for Bio-Medical Research, 4-3-2 Asahigaoka, Hino-shi, Tokyo 191-8512, Japan.

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)

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 37.9 kDa 
• Atom Count: 2,702 
• 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: MIF, GLIF, 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6UV	G [auth A]	(2~{R})-2-[[4-[[2,4-bis(azanyl)pteridin-6-yl]methyl-methyl-amino]phenyl]carbonylamino]pentanedioic acid C20 H22 N8 O5 FBOZXECLQNJBKD-CYBMUJFWSA-N
SO4	D [auth A], E [auth A], F [auth A], H [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.227 
• R-Value Work: 0.180 
• R-Value Observed: 0.183 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.758	α = 90
b = 95.758	β = 90
c = 104.154	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data processing
HKL-2000	data scaling
HKL-2000	data reduction
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL	data reduction
HKL	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-07-25 
Deposition Author(s): Takimoto-Kamimura, M., Fukushima, K.
• This entry supersedes: 5CG4

Revision History  

• Version 1.0: 2018-07-25
  Type: Initial release
  
• Version 1.1: 2021-03-10
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description