4GRQ | pdb_00004grq

Characterization of N- and C- terminus mutants of human MIF

• PDB DOI: https://doi.org/10.2210/pdb4GRQ/pdb

• Classification: cytokine, Isomerase
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-08-26 Released: 2013-10-02 
• Deposition Author(s): Fan, C., Lolis, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.161 (Depositor), 0.169 (DCC) 
• R-Value Work: 
  0.137 (Depositor) 
• R-Value Observed: 
  0.139 (Depositor) 

Starting Model: experimental

Literature

Characterization of N- and C- terminus mutants of human MIF

Fan, C., Lolis, E.

To be published.

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: 38.03 kDa 
• Atom Count: 3,222 
• Modeled Residue Count: 348 
• Deposited Residue Count: 348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage migration inhibitory factor	A, B, C	116	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
AVL	K [auth C]	2-methyl-1-[2-(propan-2-yl)pyrazolo[1,5-a]pyridin-3-yl]propan-1-one C14 H18 N2 O ZJVFLBOZORBYFE-UHFFFAOYSA-N
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	D [auth A], E [auth A], G [auth B], H [auth B], I [auth C], J [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
AVL	BindingDB:  4GRQ	Ki: 3.09e+4 (nM) from 1 assay(s)
		Kd: 1400 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.161 (Depositor), 0.169 (DCC) 
• R-Value Work:  0.137 (Depositor) 
• R-Value Observed: 0.139 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.369	α = 90
b = 95.369	β = 90
c = 103.83	γ = 120

Software Package:

Software Name	Purpose
CBASS	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-02 
Deposition Author(s): Fan, C., Lolis, E.

Revision History  

• Version 1.0: 2013-10-02
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2026-03-04
  Changes: Refinement description, Structure summary