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- PDB-7qy2: X-ray structure of furin in complex with the dichlorophenylpyridi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7qy2 | ||||||
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Title | X-ray structure of furin in complex with the dichlorophenylpyridine-based inhibitor 2 | ||||||
![]() | Furin | ||||||
![]() | HYDROLASE / proprotein convertase / inhibitor / SARS-CoV-2 / protease / complex / furin | ||||||
Function / homology | ![]() furin / nerve growth factor production / dibasic protein processing / plasma lipoprotein particle remodeling / NGF processing / Assembly of active LPL and LIPC lipase complexes / 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 ...furin / nerve growth factor production / dibasic protein processing / plasma lipoprotein particle remodeling / NGF processing / Assembly of active LPL and LIPC lipase complexes / 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 / peptide biosynthetic process / cytokine precursor processing / Pre-NOTCH Processing in Golgi / secretion by cell / Synthesis and processing of ENV and VPU / Formation of the cornified envelope / nerve growth factor binding / Signaling by PDGF / trans-Golgi network transport vesicle / Elastic fibre formation / heparan sulfate binding / Signaling by NODAL / blastocyst formation / Respiratory syncytial virus (RSV) attachment and entry / regulation of endopeptidase activity / positive regulation of membrane protein ectodomain proteolysis / peptide hormone processing / zymogen activation / CD163 mediating an anti-inflammatory response / regulation of protein catabolic process / Activation of Matrix Metalloproteinases / Maturation of hRSV A proteins / TGF-beta receptor signaling activates SMADs / Uptake and function of anthrax toxins / Collagen degradation / protein maturation / 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 / transforming growth factor beta receptor signaling pathway / extracellular matrix organization / peptide binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / trans-Golgi network / protein processing / Golgi lumen / serine-type endopeptidase inhibitor activity / heparin binding / peptidase activity / endopeptidase activity / Potential therapeutics for SARS / protease binding / viral translation / amyloid fibril formation / Induction of Cell-Cell Fusion / Attachment and Entry / endosome membrane / positive regulation of viral entry into host cell / viral protein processing / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dahms, S.O. / Brandstetter, H. / Pautsch, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Dichlorophenylpyridine-Based Molecules Inhibit Furin through an Induced-Fit Mechanism. Authors: Dahms, S.O. / Schnapp, G. / Winter, M. / Buttner, F.H. / Schleputz, M. / Gnamm, C. / Pautsch, A. / Brandstetter, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 372.7 KB | Display | ![]() |
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PDB format | ![]() | 255 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 745.4 KB | Display | ![]() |
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Full document | ![]() | 747.1 KB | Display | |
Data in XML | ![]() | 23.8 KB | Display | |
Data in CIF | ![]() | 37.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qxyC ![]() 7qxzC ![]() 7qy0C ![]() 7qy1C ![]() 5jxgS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 52112.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#7: Sugar | ChemComp-NAG / |
-Non-polymers , 6 types, 476 molecules ![](data/chem/img/I0Q.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
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![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/NA.gif)
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![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-I0Q / ( | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-DMS / #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.71 Å3/Da / Density % sol: 66.87 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: CRYSTALLIZATION SOLUTION: 100mM MES, 200mM K/NAH2PO4, PH 5.5, 2 M NACL; RESERVOIR SOLUTION: 3.0-3.2M NACL |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Dec 2, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→47.1 Å / Num. obs: 112264 / % possible obs: 98.1 % / Redundancy: 20.1 % / Biso Wilson estimate: 20.85 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.266 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.55→1.64 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 17633 / CC1/2: 0.232 / Rrim(I) all: 5.521 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5jxg Resolution: 1.55→45.89 Å / SU ML: 0.2308 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.2413 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→45.89 Å
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Refine LS restraints |
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LS refinement shell |
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