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Yorodumi- PDB-4k5z: Crystal Structure of Human Chymase in Complex with Fragment Inhib... -
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-Basic information
Entry | Database: PDB / ID: 4k5z | ||||||
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Title | Crystal Structure of Human Chymase in Complex with Fragment Inhibitor 6-chloro-2,3-dihydro-1H-isoindol-1-one | ||||||
Components | Chymase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / serine protease / glycosylated / Mast cells / secreted / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information chymase / basement membrane disassembly / cytokine precursor processing / peptide metabolic process / midbrain development / Activation of Matrix Metalloproteinases / extracellular matrix disassembly / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / serine-type peptidase activity ...chymase / basement membrane disassembly / cytokine precursor processing / peptide metabolic process / midbrain development / Activation of Matrix Metalloproteinases / extracellular matrix disassembly / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / serine-type peptidase activity / secretory granule / cellular response to glucose stimulus / peptide binding / Signaling by SCF-KIT / protein catabolic process / cytoplasmic ribonucleoprotein granule / positive regulation of angiogenesis / regulation of inflammatory response / collagen-containing extracellular matrix / endopeptidase activity / intracellular membrane-bounded organelle / serine-type endopeptidase activity / extracellular space / extracellular region / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å | ||||||
Authors | Collins, B.K. / Padyana, A.K. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Discovery of Potent, Selective Chymase Inhibitors via Fragment Linking Strategies. Authors: Taylor, S.J. / Padyana, A.K. / Abeywardane, A. / Liang, S. / Hao, M.H. / De Lombaert, S. / Proudfoot, J. / Farmer, B.S. / Li, X. / Collins, B. / Martin, L. / Albaugh, D.R. / Hill-Drzewi, M. ...Authors: Taylor, S.J. / Padyana, A.K. / Abeywardane, A. / Liang, S. / Hao, M.H. / De Lombaert, S. / Proudfoot, J. / Farmer, B.S. / Li, X. / Collins, B. / Martin, L. / Albaugh, D.R. / Hill-Drzewi, M. / Pullen, S.S. / Takahashi, H. #1: Journal: Bioorg.Med.Chem.Lett. / Year: 2011 Title: Benzimidazolone as potent chymase inhibitor: modulation of reactive metabolite formation in the hydrophobic (P1) region. Authors: Lo, H.Y. / Nemoto, P.A. / Kim, J.M. / Hao, M.H. / Qian, K.C. / Farrow, N.A. / Albaugh, D.R. / Fowler, D.M. / Schneiderman, R.D. / Michael August, E. / Martin, L. / Hill-Drzewi, M. / Pullen, ...Authors: Lo, H.Y. / Nemoto, P.A. / Kim, J.M. / Hao, M.H. / Qian, K.C. / Farrow, N.A. / Albaugh, D.R. / Fowler, D.M. / Schneiderman, R.D. / Michael August, E. / Martin, L. / Hill-Drzewi, M. / Pullen, S.S. / Takahashi, H. / De Lombaert, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k5z.cif.gz | 59.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k5z.ent.gz | 45.6 KB | Display | PDB format |
PDBx/mmJSON format | 4k5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k5z_validation.pdf.gz | 457.6 KB | Display | wwPDB validaton report |
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Full document | 4k5z_full_validation.pdf.gz | 458.4 KB | Display | |
Data in XML | 4k5z_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 4k5z_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/4k5z ftp://data.pdbj.org/pub/pdb/validation_reports/k5/4k5z | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24991.857 Da / Num. of mol.: 1 / Fragment: UNP residues 22-247 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CMA1, CYH, CYM / Plasmid: pDest1393 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P23946, chymase |
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#2: Sugar | ChemComp-NAG / |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-1P7 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.73 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8 Details: 26-33% PEG8000, 0.1 M Tris, pH 8.0, 2 mM zinc sulfate, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: Jan 15, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→74.61 Å / Num. obs: 25581 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.43 % / Rmerge(I) obs: 0.079 / Χ2: 0.93 / Net I/σ(I): 12.1 / Scaling rejects: 664 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→74.609 Å / Occupancy max: 1 / Occupancy min: 0.42 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.02 / Stereochemistry target values: ML
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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 max: 76.94 Å2 / Biso mean: 25.6311 Å2 / Biso min: 10.88 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→74.609 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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