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- PDB-7edq: MIF complex to compound7 -

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Basic information

Entry
Database: PDB / ID: 7edq
TitleMIF complex to compound7
ComponentsMacrophage migration inhibitory factor
KeywordsISOMERASE / tautomerase
Function / homology
Function and homology information


positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / dopachrome isomerase activity / phenylpyruvate tautomerase / L-dopachrome isomerase / phenylpyruvate tautomerase activity / positive regulation of arachidonate secretion / cytokine receptor binding / negative regulation of myeloid cell apoptotic process / negative regulation of macrophage chemotaxis ...positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / dopachrome isomerase activity / phenylpyruvate tautomerase / L-dopachrome isomerase / phenylpyruvate tautomerase activity / positive regulation of arachidonate secretion / cytokine receptor binding / negative regulation of myeloid cell apoptotic process / negative regulation of macrophage chemotaxis / negative regulation of mature B cell apoptotic process / carboxylic acid metabolic process / positive regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 2 production / prostaglandin biosynthetic process / negative regulation of protein metabolic process / regulation of macrophage activation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / chemoattractant activity / protein homotrimerization / negative regulation of DNA damage response, signal transduction by p53 class mediator / positive regulation of cAMP/PKA signal transduction / negative regulation of cellular senescence / positive regulation of phosphorylation / positive regulation of B cell proliferation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of cell migration / positive regulation of cytokine production / cytokine activity / Cell surface interactions at the vascular wall / DNA damage response, signal transduction by p53 class mediator / positive regulation of fibroblast proliferation / positive regulation of tumor necrosis factor production / cellular senescence / protease binding / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / inflammatory response / negative regulation of gene expression / innate immune response / positive regulation of cell population proliferation / Neutrophil degranulation / negative regulation of apoptotic process / cell surface / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Macrophage migration inhibitory factor, conserved site / Macrophage migration inhibitory factor family signature. / Macrophage migration inhibitory factor / Macrophage migration inhibitory factor (MIF) / Tautomerase/MIF superfamily
Similarity search - Domain/homology
6,7-bis(oxidanyl)chromen-2-one / Macrophage migration inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.266 Å
AuthorsFan, C.P. / Guo, D.Y. / Yang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31570762 China
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2022
Title: Repurposing old drugs as novel inhibitors of human MIF from structural and functional analysis.
Authors: Yang, L. / Yang, C. / Wang, L. / Yang, Z. / Guo, D. / Fan, C.
History
DepositionMar 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Macrophage migration inhibitory factor
B: Macrophage migration inhibitory factor
C: Macrophage migration inhibitory factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,52712
Polymers37,0653
Non-polymers4629
Water8,035446
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7740 Å2
ΔGint-123 kcal/mol
Surface area12990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.581, 68.472, 86.294
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 12 or resid 14...
21(chain B and (resid 1 through 12 or resid 14...
31(chain C and (resid 1 through 12 or resid 14...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROALAALA(chain A and (resid 1 through 12 or resid 14...AA1 - 121 - 12
12VALVALLEULEU(chain A and (resid 1 through 12 or resid 14...AA14 - 1914 - 19
13GLUGLUALAALA(chain A and (resid 1 through 12 or resid 14...AA21 - 2721 - 27
14GLNGLNGLNGLN(chain A and (resid 1 through 12 or resid 14...AA2828
15PROPROALAALA(chain A and (resid 1 through 12 or resid 14...AA1 - 1141 - 114
16PROPROALAALA(chain A and (resid 1 through 12 or resid 14...AA1 - 1141 - 114
17PROPROALAALA(chain A and (resid 1 through 12 or resid 14...AA1 - 1141 - 114
18PROPROALAALA(chain A and (resid 1 through 12 or resid 14...AA1 - 1141 - 114
19PROPROALAALA(chain A and (resid 1 through 12 or resid 14...AA1 - 1141 - 114
21PROPROALAALA(chain B and (resid 1 through 12 or resid 14...BB1 - 121 - 12
22VALVALLEULEU(chain B and (resid 1 through 12 or resid 14...BB14 - 1914 - 19
23GLUGLUSERSER(chain B and (resid 1 through 12 or resid 14...BB21 - 5221 - 52
24PROPROALAALA(chain B and (resid 1 through 12 or resid 14...BB1 - 1141 - 114
25PROPROALAALA(chain B and (resid 1 through 12 or resid 14...BB1 - 1141 - 114
26PROPROALAALA(chain B and (resid 1 through 12 or resid 14...BB1 - 1141 - 114
27PROPROALAALA(chain B and (resid 1 through 12 or resid 14...BB1 - 1141 - 114
28PROPROALAALA(chain B and (resid 1 through 12 or resid 14...BB1 - 1141 - 114
29PROPROALAALA(chain B and (resid 1 through 12 or resid 14...BB1 - 1141 - 114
31PROPROALAALA(chain C and (resid 1 through 12 or resid 14...CC1 - 121 - 12
32VALVALLEULEU(chain C and (resid 1 through 12 or resid 14...CC14 - 1914 - 19
33GLUGLUALAALA(chain C and (resid 1 through 12 or resid 14...CC21 - 2721 - 27
34PROPROALAALA(chain C and (resid 1 through 12 or resid 14...CC1 - 1141 - 114
35PROPROALAALA(chain C and (resid 1 through 12 or resid 14...CC1 - 1141 - 114
36PROPROALAALA(chain C and (resid 1 through 12 or resid 14...CC1 - 1141 - 114
37PROPROALAALA(chain C and (resid 1 through 12 or resid 14...CC1 - 1141 - 114
38PROPROALAALA(chain C and (resid 1 through 12 or resid 14...CC1 - 1141 - 114

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Components

#1: Protein Macrophage migration inhibitory factor / MIF / Glycosylation-inhibiting factor / GIF / L-dopachrome isomerase / L-dopachrome tautomerase / ...MIF / Glycosylation-inhibiting factor / GIF / L-dopachrome isomerase / L-dopachrome tautomerase / Phenylpyruvate tautomerase


Mass: 12355.056 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MIF, GLIF, MMIF / Production host: Escherichia coli (E. coli)
References: UniProt: P14174, phenylpyruvate tautomerase, L-dopachrome isomerase
#2: Chemical ChemComp-HFC / 6,7-bis(oxidanyl)chromen-2-one


Mass: 178.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.33 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.0M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.266→43.147 Å / Num. obs: 107167 / % possible obs: 100 % / Redundancy: 10.5 % / Biso Wilson estimate: 13.89 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.018 / Rrim(I) all: 0.059 / Rsym value: 0.057 / Net I/av σ(I): 18.3 / Net I/σ(I): 18.3
Reflection shellResolution: 1.27→1.29 Å / Redundancy: 8.1 % / Rmerge(I) obs: 1.435 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5219 / CC1/2: 0.553 / Rpim(I) all: 0.553 / Rrim(I) all: 0.528 / Rsym value: 1.435 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MIF

1mif


Resolution: 1.266→43.147 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1898 2009 1.88 %
Rwork0.1698 105073 -
obs0.1702 107082 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 49.91 Å2 / Biso mean: 19.8013 Å2 / Biso min: 7.78 Å2
Refinement stepCycle: final / Resolution: 1.266→43.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2590 0 21 446 3057
Biso mean--33.06 30.19 -
Num. residues----342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122692
X-RAY DIFFRACTIONf_angle_d1.1033671
X-RAY DIFFRACTIONf_chiral_restr0.107405
X-RAY DIFFRACTIONf_plane_restr0.008484
X-RAY DIFFRACTIONf_dihedral_angle_d8.6261558
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1531X-RAY DIFFRACTION7.372TORSIONAL
12B1531X-RAY DIFFRACTION7.372TORSIONAL
13C1531X-RAY DIFFRACTION7.372TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.266-1.29720.35391390.36857404
1.2972-1.33230.43211470.29777402
1.3323-1.37150.34451420.28347454
1.3715-1.41580.28011420.23957432
1.4158-1.46640.23371400.20977428
1.4664-1.52510.21061410.18287460
1.5251-1.59450.1931470.17827463
1.5945-1.67860.18551380.15987453
1.6786-1.78380.23571430.16577491
1.7838-1.92150.1631400.15177511
1.9215-2.11490.19511440.14577528
2.1149-2.42090.16561420.15487550
2.4209-3.04990.16971490.17217606
3.0499-43.1470.16631550.15377891

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