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Yorodumi- PDB-4omc: X-ray structure of human furin in complex with the competitive in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4omc | ||||||
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Title | X-ray structure of human furin in complex with the competitive inhibitor meta-guanidinomethyl-Phac-RVR-Amba | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / pro-protein convertase / serine protease / competitive inhibitor / protease-inhibitor complex / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information furin / nerve growth factor production / dibasic protein processing / plasma lipoprotein particle remodeling / NGF processing / Assembly of active LPL and LIPC lipase complexes / peptide biosynthetic process / negative regulation of transforming growth factor beta1 production / signal peptide processing / regulation of cholesterol transport ...furin / nerve growth factor production / dibasic protein processing / plasma lipoprotein particle remodeling / NGF processing / Assembly of active LPL and LIPC lipase complexes / peptide biosynthetic process / negative regulation of transforming growth factor beta1 production / signal peptide processing / regulation of cholesterol transport / negative regulation of low-density lipoprotein particle receptor catabolic process / cytokine precursor processing / Pre-NOTCH Processing in Golgi / secretion by cell / Synthesis and processing of ENV and VPU / nerve growth factor binding / Formation of the cornified envelope / Signaling by PDGF / trans-Golgi network transport vesicle / blastocyst formation / Elastic fibre formation / heparan sulfate binding / Signaling by NODAL / positive regulation of membrane protein ectodomain proteolysis / zymogen activation / regulation of endopeptidase activity / peptide hormone processing / CD163 mediating an anti-inflammatory response / regulation of protein catabolic process / Activation of Matrix Metalloproteinases / TGF-beta receptor signaling activates SMADs / protein maturation / Uptake and function of anthrax toxins / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / regulation of signal transduction / Removal of aminoterminal propeptides from gamma-carboxylated proteins / negative regulation of inflammatory response to antigenic stimulus / viral life cycle / serine-type peptidase activity / extracellular matrix organization / transforming growth factor beta receptor signaling pathway / peptide binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / trans-Golgi network / serine-type endopeptidase inhibitor activity / protein processing / Golgi lumen / heparin binding / peptidase activity / viral translation / endopeptidase activity / Induction of Cell-Cell Fusion / protease binding / amyloid fibril formation / Potential therapeutics for SARS / Attachment and Entry / positive regulation of viral entry into host cell / viral protein processing / endosome membrane / membrane raft / Amyloid fiber formation / Golgi membrane / serine-type endopeptidase activity / cell surface / endoplasmic reticulum / extracellular exosome / extracellular region / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Dahms, S.O. / Than, M.E. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2014 Title: X-ray Structures of Human Furin in Complex with Competitive Inhibitors. Authors: Dahms, S.O. / Hardes, K. / Becker, G.L. / Steinmetzer, T. / Brandstetter, H. / Than, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4omc.cif.gz | 567.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4omc.ent.gz | 478.8 KB | Display | PDB format |
PDBx/mmJSON format | 4omc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/4omc ftp://data.pdbj.org/pub/pdb/validation_reports/om/4omc | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 12 molecules ABCDEFHIJKLN
#1: Protein | Mass: 52388.602 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 108-574 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FUR, FURIN, PACE, PCSK3 / Plasmid: pHLsec / Cell (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P09958, furin #2: Protein/peptide | |
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-Non-polymers , 4 types, 1394 molecules
#3: Chemical | ChemComp-FMT / #4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-NA / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 50mM Tris, 2.8M sodium formate, 0.015mM Cymal-7, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2013 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 161839 / Num. obs: 160915 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 31.4 Å2 / Rsym value: 0.012 / Net I/σ(I): 9.69 |
Reflection shell | Resolution: 2.3→2.44 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.63 / Num. unique all: 25523 / Rsym value: 0.051 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.4 Å
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