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Yorodumi- PDB-6yd3: X-ray structure of furin in complex with the canavanine derived i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yd3 | ||||||||||||
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Title | X-ray structure of furin in complex with the canavanine derived inhibitor 4-guanidinomethyl-phenylacetyl-Canavanine-Tle-Arg-Amba | ||||||||||||
Components |
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Keywords | HYDROLASE / Protease / Inhibitor / Complex / Canavanine | ||||||||||||
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 / 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 / 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 / Signaling by NODAL / blastocyst formation / 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 / Respiratory syncytial virus (RSV) attachment and entry / 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 / 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 / peptidase activity / heparin binding / 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) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||||||||
Authors | Dahms, S.O. | ||||||||||||
Funding support | Austria, 1items
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Citation | Journal: Acs Med.Chem.Lett. / Year: 2021 Title: The Basicity Makes the Difference: Improved Canavanine-Derived Inhibitors of the Proprotein Convertase Furin. Authors: Lam van, T.V. / Heindl, M.R. / Schlutt, C. / Bottcher-Friebertshauser, E. / Bartenschlager, R. / Klebe, G. / Brandstetter, H. / Dahms, S.O. / Steinmetzer, T. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yd3.cif.gz | 343.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yd3.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6yd3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yd3_validation.pdf.gz | 453.2 KB | Display | wwPDB validaton report |
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Full document | 6yd3_full_validation.pdf.gz | 454.1 KB | Display | |
Data in XML | 6yd3_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 6yd3_validation.cif.gz | 35.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/6yd3 ftp://data.pdbj.org/pub/pdb/validation_reports/yd/6yd3 | HTTPS FTP |
-Related structure data
Related structure data | 6yd2C 6yd4C 6yd7C 5jxhS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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 / Protein/peptide , 2 types, 2 molecules A611
#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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#2: Protein/peptide | Mass: 738.903 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 6 types, 427 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CL / | #6: Chemical | #7: Chemical | ChemComp-DMS / | #8: 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 | Density Matthews: 3.72 Å3/Da / Density % sol: 66.96 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: CRYSTALLIZATION SOLUTION: 100MM MES, 200MM K/NAH2PO4, PH 5.5-6.0, 2 M NACL; RESERVOIR SOLUTION: 3-4M NACL |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 30, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2→43.1 Å / Num. obs: 52910 / % possible obs: 97.9 % / Redundancy: 17.1 % / Biso Wilson estimate: 26.88 Å2 / Rrim(I) all: 0.214 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2→2.12 Å / Num. unique obs: 8463 / Rrim(I) all: 1.398 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JXH Resolution: 2→43.06 Å / SU ML: 0.167 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.8774
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→43.06 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 35.1950177324 Å / Origin y: -37.5603390363 Å / Origin z: 0.284230597584 Å
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Refinement TLS group | Selection details: chain A |