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Yorodumi- PDB-7cm0: Crystal structure of a glutaminyl cyclase in complex with NHV-1009 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cm0 | ||||||
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Title | Crystal structure of a glutaminyl cyclase in complex with NHV-1009 | ||||||
Components | Glutaminyl-peptide cyclotransferase | ||||||
Keywords | TRANSFERASE / glutaminyl cyclases (QCs) / Alzheimer disease | ||||||
Function / homology | Function and homology information peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase activity / protein modification process / specific granule lumen / tertiary granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / extracellular exosome / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Lee, J.W. / Song, J.Y. / Jang, T.H. / Ha, J.H. | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2021 Title: Discovery of highly potent human glutaminyl cyclase (QC) inhibitors as anti-Alzheimer's agents by the combination of pharmacophore-based and structure-based design. Authors: Van Manh, N. / Hoang, V.H. / Ngo, V.T.H. / Ann, J. / Jang, T.H. / Ha, J.H. / Song, J.Y. / Ha, H.J. / Kim, H. / Kim, Y.H. / Lee, J. / Lee, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cm0.cif.gz | 270.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cm0.ent.gz | 215.2 KB | Display | PDB format |
PDBx/mmJSON format | 7cm0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/7cm0 ftp://data.pdbj.org/pub/pdb/validation_reports/cm/7cm0 | HTTPS FTP |
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-Related structure data
Related structure data | 4ywyS S: Starting model for refinement |
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Similar 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 37399.242 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: QPCT / Production host: Escherichia coli (E. coli) References: UniProt: Q16769, glutaminyl-peptide cyclotransferase #2: Chemical | ChemComp-G5R / #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | 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: 2.62 Å3/Da / Density % sol: 53.1 % |
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Crystal grow | Temperature: 291 K / Method: liquid diffusion / Details: 4M Ammonium acetate, pH 7.0, 0.1M Bis-Tris propane |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→35.47 Å / Num. obs: 77174 / % possible obs: 99.46 % / Redundancy: 11.5 % / CC1/2: 0.861 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.2→2.279 Å / Num. unique obs: 35430 / CC1/2: 0.861 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YWY Resolution: 2.2→33.74 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 44.65 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→33.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.279 Å
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