+Open data
-Basic information
Entry | Database: PDB / ID: 4cib | |||||||||
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Title | crystal structure of cathepsin a, complexed with compound 2 | |||||||||
Components | LYSOSOMAL PROTECTIVE PROTEIN | |||||||||
Keywords | HYDROLASE / DRUG DISCOVERY / SERINE CARBOXYPEPTIDASE / CARDIOVASCULAR DRUG / HEART FAILURE / ENDOTHELIN / TETRAHEDRAL INTERMEDIATE / COVALENT INHIBITOR | |||||||||
Function / homology | Function and homology information carboxypeptidase C / Defective NEU1 causes sialidosis / serine-type carboxypeptidase activity / Sialic acid metabolism / regulation of chaperone-mediated autophagy / Glycosphingolipid catabolism / negative regulation of chaperone-mediated autophagy / carboxypeptidase activity / enzyme activator activity / MHC class II antigen presentation ...carboxypeptidase C / Defective NEU1 causes sialidosis / serine-type carboxypeptidase activity / Sialic acid metabolism / regulation of chaperone-mediated autophagy / Glycosphingolipid catabolism / negative regulation of chaperone-mediated autophagy / carboxypeptidase activity / enzyme activator activity / MHC class II antigen presentation / lysosomal lumen / intracellular protein transport / regulation of protein stability / azurophil granule lumen / lysosome / intracellular membrane-bounded organelle / Neutrophil degranulation / endoplasmic reticulum / proteolysis / extracellular exosome / extracellular region / membrane Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | |||||||||
Authors | Schreuder, H.A. / Liesum, A. / Kroll, K. / Boehnisch, B. / Buning, C. / Ruf, S. / Buning, C. / Sadowski, T. | |||||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2014 Title: Crystal structure of cathepsin A, a novel target for the treatment of cardiovascular diseases. Authors: Schreuder, H.A. / Liesum, A. / Kroll, K. / Bohnisch, B. / Buning, C. / Ruf, S. / Sadowski, T. #1: Journal: J.Med.Chem. / Year: 2012 Title: Novel Beta-Amino Acid Derivatives as Inhibitors of Cathepsin A. Authors: Ruf, S. / Buning, C. / Schreuder, H. / Horstick, G. / Linz, W. / Olpp, T. / Pernerstorfer, J. / Hiss, K. / Kroll, K. / Kannt, A. / Kohlmann, M. / Linz, D. / Hubschle, T. / Rutten, H. / ...Authors: Ruf, S. / Buning, C. / Schreuder, H. / Horstick, G. / Linz, W. / Olpp, T. / Pernerstorfer, J. / Hiss, K. / Kroll, K. / Kannt, A. / Kohlmann, M. / Linz, D. / Hubschle, T. / Rutten, H. / Wirth, K. / Schmidt, T. / Sadowski, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cib.cif.gz | 124.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cib.ent.gz | 92.4 KB | Display | PDB format |
PDBx/mmJSON format | 4cib.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cib_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4cib_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4cib_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 4cib_validation.cif.gz | 44.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/4cib ftp://data.pdbj.org/pub/pdb/validation_reports/ci/4cib | HTTPS FTP |
-Related structure data
Related structure data | 4ci9C 4ciaC 4az0S C: citing same article (ref.) 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 51829.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: ACTIVATED WITH TRYPSIN-SEPHAROSE / Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P10619, carboxypeptidase C | ||||||||
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#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-7UZ / | #4: Chemical | ChemComp-CD / #5: Water | ChemComp-HOH / | Sequence details | 2 EXTRA RESIDUES FROM PREPROMELLITIN SIGNAL SEQUENCE AT N- TERMINUS AND 1 EXTRA RESIDUE, LEFT OVER ...2 EXTRA RESIDUES FROM PREPROMELL | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.2 % / Description: NONE |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: CATHEPSIN A WAS CRYSTALLIZED USING THE HANGING DROP METHOD: 1 UL OF PROTEIN SOLUTION, CONTAINING 6.5 MG/ML CATHEPSIN A, 25 MM TRIS-HCL (PH 8.0) AND 300 MM NACL, WAS MIXED WITH 1 UL RESERVOIR ...Details: CATHEPSIN A WAS CRYSTALLIZED USING THE HANGING DROP METHOD: 1 UL OF PROTEIN SOLUTION, CONTAINING 6.5 MG/ML CATHEPSIN A, 25 MM TRIS-HCL (PH 8.0) AND 300 MM NACL, WAS MIXED WITH 1 UL RESERVOIR SOLUTION, CONTAINING 100 MM NAACETATE (PH 4.5), 18-20% PEG400 AND 100 MM CDCL2, AND SET TO EQUILIBRATE AT 4DEG.C. ROD-SHAPED CRYSTALS APPEARED IN ABOUT ONE WEEK. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 29, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→66.74 Å / Num. obs: 35026 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.12 |
Reflection shell | Resolution: 1.89→1.94 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.76 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AZ0 Resolution: 1.89→44.02 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.815 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.551 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→44.02 Å
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Refine LS restraints |
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