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Yorodumi- PDB-7qxy: X-ray structure of furin in complex with the dichlorophenylpyridi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qxy | ||||||
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Title | X-ray structure of furin in complex with the dichlorophenylpyridine-based inhibitor 3 | ||||||
Components | Furin | ||||||
Keywords | HYDROLASE / proprotein convertase / inhibitor / SARS-CoV-2 / protease / complex / furin | ||||||
Function / homology | Function and homology information furin / nerve growth factor production / dibasic protein processing / plasma lipoprotein particle remodeling / NGF processing / cytokine precursor processing / Assembly of active LPL and LIPC lipase complexes / 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 / cytokine precursor 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 / Pre-NOTCH Processing in Golgi / secretion by cell / nerve growth factor binding / Synthesis and processing of ENV and VPU / Formation of the cornified envelope / Signaling by PDGF / trans-Golgi network transport vesicle / Elastic fibre formation / heparan sulfate binding / blastocyst formation / Signaling by NODAL / regulation of endopeptidase activity / peptide hormone processing / zymogen activation / positive regulation of membrane protein ectodomain proteolysis / 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 / protein maturation / Uptake and function of anthrax toxins / Respiratory syncytial virus (RSV) attachment and entry / 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 / serine-type endopeptidase inhibitor activity / trans-Golgi network / protein processing / Golgi lumen / heparin binding / peptidase activity / protease binding / endopeptidase activity / viral translation / amyloid fibril formation / Potential therapeutics for SARS / Induction of Cell-Cell Fusion / 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: 1.478 Å | ||||||
Authors | Dahms, S.O. / Brandstetter, H. / Pautsch, A. | ||||||
Funding support | Austria, 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qxy.cif.gz | 291.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qxy.ent.gz | 237.6 KB | Display | PDB format |
PDBx/mmJSON format | 7qxy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qxy_validation.pdf.gz | 706.4 KB | Display | wwPDB validaton report |
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Full document | 7qxy_full_validation.pdf.gz | 707.1 KB | Display | |
Data in XML | 7qxy_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 7qxy_validation.cif.gz | 40.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/7qxy ftp://data.pdbj.org/pub/pdb/validation_reports/qx/7qxy | HTTPS FTP |
-Related structure data
Related structure data | 7qxzC 7qy0C 7qy1C 7qy2C 5jxgS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 52112.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FURIN, FUR, PACE, PCSK3 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P09958, furin |
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-Non-polymers , 5 types, 670 molecules
#2: Chemical | #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-I1G / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
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 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999917 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 15, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999917 Å / Relative weight: 1 |
Reflection | Resolution: 1.478→114.031 Å / Num. obs: 87795 / % possible obs: 66.5 % / Redundancy: 39.2 % / Biso Wilson estimate: 18.89 Å2 / Rmerge(I) obs: 0.207 / Rsym value: 0.207 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.478→1.654 Å / Redundancy: 29.4 % / Rmerge(I) obs: 2.845 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4388 / Rsym value: 2.845 / % possible all: 11.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5jxg Resolution: 1.478→114.03 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.955 / SU R Cruickshank DPI: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.079 / SU Rfree Blow DPI: 0.074 / SU Rfree Cruickshank DPI: 0.069 Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION. REFINEMENT NOTES. NUMBER OF REFINEMENT NOTES : 1 NOTE 1 : IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso max: 258.31 Å2 / Biso mean: 24.97 Å2 / Biso min: 7.33 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.478→114.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.48→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
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Refinement TLS params. | Method: refined / Origin x: 34.9592 Å / Origin y: -37.687 Å / Origin z: 0.4363 Å
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Refinement TLS group | Selection details: { A|* } |