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Yorodumi- PDB-1t31: A Dual Inhibitor of the Leukocyte Proteases Cathepsin G and Chyma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t31 | |||||||||
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Title | A Dual Inhibitor of the Leukocyte Proteases Cathepsin G and Chymase with Therapeutic Efficacy in Animals Models of Inflammation | |||||||||
Components | Chymase | |||||||||
Keywords | HYDROLASE / HUMAN CHYMASE / SERINE PROTEINASE | |||||||||
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 / peptide binding / secretory granule / cellular response to glucose stimulus / protein catabolic process / Signaling by SCF-KIT / cytoplasmic ribonucleoprotein granule / positive regulation of angiogenesis / regulation of inflammatory response / endopeptidase activity / collagen-containing extracellular matrix / serine-type endopeptidase activity / intracellular membrane-bounded organelle / extracellular space / extracellular region / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | de Garavilla, L. / Greco, M.N. / Giardino, E.C. / Wells, G.I. / Haertlein, B.J. / Kauffman, J.A. / Corcoran, T.W. / Derian, C.K. / Eckardt, A.J. / Abraham, W.M. ...de Garavilla, L. / Greco, M.N. / Giardino, E.C. / Wells, G.I. / Haertlein, B.J. / Kauffman, J.A. / Corcoran, T.W. / Derian, C.K. / Eckardt, A.J. / Abraham, W.M. / Sukumar, N. / Chen, Z. / Pineda, A.O. / Mathews, F.S. / Di Cera, E. / Andrade-Gordon, P. / Damiano, B.P. / Maryanoff, B.E. / Pereira, P.J.B. / Wang, Z.M. / Rubin, H. / Huber, R. / Bode, W. / Schechter, N.M. / Strobl, S. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: A novel, potent dual inhibitor of the leukocyte proteases cathepsin G and chymase: molecular mechanisms and anti-inflammatory activity in vivo. Authors: de Garavilla, L. / Greco, M.N. / Sukumar, N. / Chen, Z.W. / Pineda, A.O. / Mathews, F.S. / Di Cera, E. / Giardino, E.C. / Wells, G.I. / Haertlein, B.J. / Kauffman, J.A. / Corcoran, T.W. / ...Authors: de Garavilla, L. / Greco, M.N. / Sukumar, N. / Chen, Z.W. / Pineda, A.O. / Mathews, F.S. / Di Cera, E. / Giardino, E.C. / Wells, G.I. / Haertlein, B.J. / Kauffman, J.A. / Corcoran, T.W. / Derian, C.K. / Eckardt, A.J. / Damiano, B.P. / Andrade-Gordon, P. / Maryanoff, B.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t31.cif.gz | 71.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t31.ent.gz | 49.2 KB | Display | PDB format |
PDBx/mmJSON format | 1t31.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1t31_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1t31_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1t31_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 1t31_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t3/1t31 ftp://data.pdbj.org/pub/pdb/validation_reports/t3/1t31 | HTTPS FTP |
-Related structure data
Related structure data | 1t32C 1pjpS 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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2 |
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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: 24991.857 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CMA1, CYM, CYH / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P23946, chymase |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 229 molecules
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-CO / | #6: Chemical | ChemComp-OHH / | #7: Chemical | ChemComp-MES / | #8: Water | ChemComp-HOH / | |
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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 Å3/Da / Density % sol: 59 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion / pH: 6.5 Details: ammonium sulfate, MES, cobalt chloride, pH 6.5, VAPOR DIFFUSION, temperature 296.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 6, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. all: 24378 / Num. obs: 20258 / % possible obs: 83.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 3.7 / Num. unique all: 2394 / % possible all: 52.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PJP Resolution: 1.9→40 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 31.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→40 Å
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Refine LS restraints |
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LS refinement shell |
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