+Open data
-Basic information
Entry | Database: PDB / ID: 4z1u | ||||||
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Title | MIF in complex with 1-(4-methylphenyl)-3-phenylprop-2-yn-1-one | ||||||
Components | Macrophage migration inhibitory factor | ||||||
Keywords | ISOMERASE/ISOMERASE INHIBITOR / covalent inhibitor / protein surface modification / ISOMERASE-ISOMERASE INHIBITOR complex | ||||||
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 / phenylpyruvate tautomerase / L-dopachrome isomerase / dopachrome isomerase activity / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonic acid secretion / negative regulation of myeloid cell apoptotic process ...positive regulation of prostaglandin secretion involved in immune response / positive regulation of myeloid leukocyte cytokine production involved in immune response / phenylpyruvate tautomerase / L-dopachrome isomerase / dopachrome isomerase activity / phenylpyruvate tautomerase activity / positive regulation of lipopolysaccharide-mediated signaling pathway / cytokine receptor binding / positive regulation of arachidonic acid secretion / 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 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 / positive regulation of protein kinase A signaling / protein homotrimerization / negative regulation of cellular senescence / negative regulation of DNA damage response, signal transduction by p53 class mediator / DNA damage response, signal transduction by p53 class mediator / 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 / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-tyrosine phosphorylation / cellular senescence / positive regulation of fibroblast proliferation / positive regulation of peptidyl-serine phosphorylation / secretory granule lumen / protease binding / vesicle / ficolin-1-rich granule lumen / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Cho, T.Y. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Cell. Mol. Med. / Year: 2017 Title: Structural basis for decreased induction of class IB PI3-kinases expression by MIF inhibitors. Authors: Singh, A.K. / Pantouris, G. / Borosch, S. / Rojanasthien, S. / Cho, T.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z1u.cif.gz | 152.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z1u.ent.gz | 120.6 KB | Display | PDB format |
PDBx/mmJSON format | 4z1u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4z1u_validation.pdf.gz | 498.7 KB | Display | wwPDB validaton report |
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Full document | 4z1u_full_validation.pdf.gz | 515.2 KB | Display | |
Data in XML | 4z1u_validation.xml.gz | 34.8 KB | Display | |
Data in CIF | 4z1u_validation.cif.gz | 46.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z1/4z1u ftp://data.pdbj.org/pub/pdb/validation_reports/z1/4z1u | HTTPS FTP |
-Related structure data
Related structure data | 4z15C 4z1tC 1mifS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 12575.322 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MIF, GLIF, MMIF / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P14174, phenylpyruvate tautomerase, L-dopachrome isomerase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Compound details | The polypeptide, Macrophage migration inhibitory factor, with PRO at the N-terminus was incubated ...The polypeptide, Macrophage migration inhibitory factor, with PRO at the N-terminus was incubated with 1-(4-methylphenyl)-3-phenylprop-2-yn-1-one to produce the modified N-terminal residue (4N7) | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.57 Å3/Da / Density % sol: 65.51 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: Tris, ammonium sulfate, isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 31, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→75.2 Å / Num. obs: 68188 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rsym value: 0.101 / Net I/σ(I): 6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MIF Resolution: 2.05→47.66 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.877 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.268 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→47.66 Å
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