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Yorodumi- PDB-5om9: Crystal structure of the human CARBOXYPEPTIDASE A1 in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5om9 | |||||||||
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Title | Crystal structure of the human CARBOXYPEPTIDASE A1 in complex with a thiirane mechanism-based inhibitor | |||||||||
Components | Carboxypeptidase A1 | |||||||||
Keywords | HYDROLASE | |||||||||
Function / homology | Function and homology information carboxypeptidase A / leukotriene metabolic process / metallocarboxypeptidase activity / response to cadmium ion / proteolysis involved in protein catabolic process / proteolysis / extracellular space / zinc ion binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Gallego, P. / Granados, C. / Fernandez, D. / Pallares, I. / Covaleda, G. / Aviles, F.X. / Vendrell, J. / Reverter, D. | |||||||||
Citation | Journal: ACS Med Chem Lett / Year: 2017 Title: Discovery of Mechanism-Based Inactivators for Human Pancreatic Carboxypeptidase A from a Focused Synthetic Library. Authors: Testero, S.A. / Granados, C. / Fernandez, D. / Gallego, P. / Covaleda, G. / Reverter, D. / Vendrell, J. / Aviles, F.X. / Pallares, I. / Mobashery, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5om9.cif.gz | 339.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5om9.ent.gz | 274.9 KB | Display | PDB format |
PDBx/mmJSON format | 5om9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5om9_validation.pdf.gz | 459.4 KB | Display | wwPDB validaton report |
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Full document | 5om9_full_validation.pdf.gz | 471.8 KB | Display | |
Data in XML | 5om9_validation.xml.gz | 34.2 KB | Display | |
Data in CIF | 5om9_validation.cif.gz | 50.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/5om9 ftp://data.pdbj.org/pub/pdb/validation_reports/om/5om9 | HTTPS FTP |
-Related structure data
Related structure data | 2v77S 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
#1: Protein | Mass: 47190.027 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CPA1, CPA / Production host: Escherichia coli (E. coli) / References: UniProt: P15085, carboxypeptidase A #2: Chemical | #3: Chemical | #4: 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: 2 Å3/Da / Density % sol: 38.6 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 20% PEG 6000, 0.2M MGCL2, 0.1 M TRIS- HCL BUFFER PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→44.5 Å / Num. obs: 69096 / % possible obs: 94.1 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.77→1.86 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 4.2 / % possible all: 66 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2V77 Resolution: 1.8→43.68 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.357 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.465 / ESU R Free: 0.128 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.127 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→43.68 Å
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Refine LS restraints |
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