[English] 日本語
Yorodumi- PDB-6b1k: Macrophage Migration Inhibitory Factor in Complex with a Naphthyr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6b1k | ||||||
---|---|---|---|---|---|---|---|
Title | Macrophage Migration Inhibitory Factor in Complex with a Naphthyridinone Inhibitor (3a) | ||||||
Components | Macrophage migration inhibitory factor | ||||||
Keywords | ISOMERASE/ISOMERASE inhibitor / CD74 BINDING / TAUTOMERASE / INHIBITOR / COMPLEX / ISOMERASE-ISOMERASE INHIBITOR COMPLEX / ISOMERASE | ||||||
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 / cytokine receptor binding / positive regulation of lipopolysaccharide-mediated signaling pathway / 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 / dopachrome isomerase activity / phenylpyruvate tautomerase / L-dopachrome isomerase / phenylpyruvate tautomerase activity / cytokine receptor binding / positive regulation of lipopolysaccharide-mediated signaling pathway / 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 / positive regulation of chemokine (C-X-C motif) ligand 2 production / negative regulation of protein metabolic process / prostaglandin biosynthetic process / carboxylic acid 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 / positive regulation of protein kinase A signaling / negative regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of cellular senescence / DNA damage response, signal transduction by p53 class mediator / positive regulation of B cell proliferation / positive regulation of phosphorylation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of cell migration / cytokine activity / positive regulation of cytokine production / Cell surface interactions at the vascular wall / positive regulation of fibroblast proliferation / positive regulation of peptidyl-tyrosine phosphorylation / cellular senescence / positive regulation of tumor necrosis factor production / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å | ||||||
Authors | Krimmer, S.G. / Robertson, M.J. / Jorgensen, W.L. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2017 Title: Adding a Hydrogen Bond May Not Help: Naphthyridinone vs Quinoline Inhibitors of Macrophage Migration Inhibitory Factor. Authors: Dawson, T.K. / Dziedzic, P. / Robertson, M.J. / Cisneros, J.A. / Krimmer, S.G. / Newton, A.S. / Tirado-Rives, J. / Jorgensen, W.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6b1k.cif.gz | 224.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6b1k.ent.gz | 185 KB | Display | PDB format |
PDBx/mmJSON format | 6b1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/6b1k ftp://data.pdbj.org/pub/pdb/validation_reports/b1/6b1k | HTTPS FTP |
---|
-Related structure data
Related structure data | 6b1cC 6b2cC 3u18S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | 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 / Plasmid: PET11B / Cell (production host): BL21 / Production host: Escherichia coli (E. coli) References: UniProt: P14174, phenylpyruvate tautomerase, L-dopachrome isomerase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 2.1 M AMMONIUM SULFATE, 0.1 M TRIS-HCL PH 7.5, 3% ISOPROPANOL, 1.4% DMSO |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.17→200 Å / Num. obs: 118139 / % possible obs: 97.9 % / Redundancy: 11.9 % / Rsym value: 0.058 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 1.17→1.23 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 16818 / Rsym value: 0.727 / % possible all: 86.8 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3U18 Resolution: 1.17→82.664 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 12.49
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.17→82.664 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|