+Open data
-Basic information
Entry | Database: PDB / ID: 5lyf | ||||||
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Title | Crystal structure of 1 in complex with tafCPB | ||||||
Components | Carboxypeptidase B | ||||||
Keywords | HYDROLASE / tafinized carboxypeptidase B / HYRDROLASE | ||||||
Function / homology | Function and homology information carboxypeptidase B / metallocarboxypeptidase activity / cytoplasmic vesicle / proteolysis / extracellular space / zinc ion binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.01 Å | ||||||
Authors | Schreuder, H. / Liesum, A. / Loenze, P. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2016 Title: Sulfamide as Zinc Binding Motif in Small Molecule Inhibitors of Activated Thrombin Activatable Fibrinolysis Inhibitor (TAFIa). Authors: Halland, N. / Czech, J. / Czechtizky, W. / Evers, A. / Follmann, M. / Kohlmann, M. / Schreuder, H.A. / Kallus, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lyf.cif.gz | 88.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lyf.ent.gz | 69.5 KB | Display | PDB format |
PDBx/mmJSON format | 5lyf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lyf_validation.pdf.gz | 728 KB | Display | wwPDB validaton report |
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Full document | 5lyf_full_validation.pdf.gz | 735.1 KB | Display | |
Data in XML | 5lyf_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 5lyf_validation.cif.gz | 33.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/5lyf ftp://data.pdbj.org/pub/pdb/validation_reports/ly/5lyf | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 34859.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: CPB1, CPB / Production host: Komagataella pastoris CBS 7435 (fungus) / References: UniProt: P09955, carboxypeptidase B | ||||
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#2: Chemical | #3: Chemical | ChemComp-7B6 / ( | #4: 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: 2.3 Å3/Da / Density % sol: 46.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: THE PURIFIED PROTEIN WAS DISSOLVED IN 50 MM TRIS-HCL, PH 7.5 AND CONCENTRATED TO 11 MG/ML. 1 UL OF PROTEIN SOLUTION WAS EQUILIBRATED AGAINST 1 UL OF RESERVOIR SOLUTIONS CONTAINING 16-20% ...Details: THE PURIFIED PROTEIN WAS DISSOLVED IN 50 MM TRIS-HCL, PH 7.5 AND CONCENTRATED TO 11 MG/ML. 1 UL OF PROTEIN SOLUTION WAS EQUILIBRATED AGAINST 1 UL OF RESERVOIR SOLUTIONS CONTAINING 16-20% PEG3350, 100 MM MES PH 5.5 AND 50 MM ZNACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 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: 2.01→81.42 Å / Num. obs: 21825 / % possible obs: 98.7 % / Observed criterion σ(F): -3 / Redundancy: 10.4 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.01→2.1 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 7.99 / % possible all: 90.7 |
-Processing
Software |
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Refinement | Resolution: 2.01→49.39 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.845 / SU B: 6.973 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.245 / 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: 21.074 Å2
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Refinement step | Cycle: 1 / Resolution: 2.01→49.39 Å
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Refine LS restraints |
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