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Yorodumi- PDB-4uee: Crystal structure of the human CARBOXYPEPTIDASE A1 in complex wit... -
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-Basic information
Entry | Database: PDB / ID: 4uee | ||||||
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Title | Crystal structure of the human CARBOXYPEPTIDASE A1 in complex with the PHOSPHINIC INHIBITOR Acetyl-Leu-Ala-Y(PO2CH2)-homoPhe-OH | ||||||
Components | CARBOXYPEPTIDASE A1 | ||||||
Keywords | HYDROLASE / CPA1 / PHOSPHINIC INHIBITOR | ||||||
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: 2.27 Å | ||||||
Authors | Gallego, P. / Covaleda, G. / Costenaro, L. / Devel, L. / Dive, V. / Aviles, F.X. / Reverter, D. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Human Carboxypeptidase A1 in Complex with Phosphinic Inhibitors Authors: Gallego, P. / Covaleda, G. / Devel, L. / Dive, V. / Aviles, F.X. / Reverter, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uee.cif.gz | 260.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uee.ent.gz | 210.1 KB | Display | PDB format |
PDBx/mmJSON format | 4uee.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uee_validation.pdf.gz | 996.4 KB | Display | wwPDB validaton report |
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Full document | 4uee_full_validation.pdf.gz | 1003.5 KB | Display | |
Data in XML | 4uee_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | 4uee_validation.cif.gz | 37.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ue/4uee ftp://data.pdbj.org/pub/pdb/validation_reports/ue/4uee | HTTPS FTP |
-Related structure data
Related structure data | 4uezC 2v77S 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
#1: Protein | Mass: 34704.840 Da / Num. of mol.: 2 / Fragment: CARBOXYPEPTIDASE DOMAIN, RESIDUES 111-4189 Source method: isolated from a genetically manipulated source Details: IN COMPLEX WITH THE PHOSPHINIC INHIBITOR ACETYL-LEU-ALA-Y(PO2CH2)-HOMOPHE-OH. Source: (gene. exp.) HOMO SAPIENS (human) / Organ: PANCREAS / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): KM71H / 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: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.11 % / Description: NONE |
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Crystal grow | Details: 0.2 M CALCIUM CHLORIDE, 0.1 M HEPES PH 7.0 AND 20% W/V PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979471 |
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: 0.979471 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→46.3 Å / Num. obs: 25246 / % possible obs: 86.6 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 5.3 / % possible all: 58.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V77 Resolution: 2.27→78.55 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.9 / SU B: 13.63 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R Free: 0.254 / 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 |
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Refinement step | Cycle: LAST / Resolution: 2.27→78.55 Å
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Refine LS restraints |
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