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Yorodumi- PDB-2pj4: CRYSTAL STRUCTURE OF ACTIVATED PORCINE PANCREATIC CARBOXYPEPTIDAS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pj4 | ||||||
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Title | CRYSTAL STRUCTURE OF ACTIVATED PORCINE PANCREATIC CARBOXYPEPTIDASE B [((R)-Benzyloxycarbonylamino-cyclohexyl-methyl)-hydroxy-phosphinoyloxy]-(3-guanidino-phenyl)-acetic acid COMPLEX | ||||||
Components | Carboxypeptidase B | ||||||
Keywords | HYDROLASE / CARBOXYPEPTIDASE B / EXOPEPTIDASE / Phosphinate BASED INHIBITOR | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Adler, M. / Whitlow, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Structures of potent selective peptide mimetics bound to carboxypeptidase B. Authors: Adler, M. / Buckman, B. / Bryant, J. / Chang, Z. / Chu, K. / Emayan, K. / Hrvatin, P. / Islam, I. / Morser, J. / Sukovich, D. / West, C. / Yuan, S. / Whitlow, M. #1: Journal: Biochemistry / Year: 2005 Title: Crystal Structures of Potent Thiol-Based Inhibitors Bound to Carboxypeptidase B. Authors: Adler, M. / Bryant, J. / Buckman, B. / Islam, I. / Larsen, B. / Finster, S. / Kent, L. / May, K. / Mohan, R. / Yuan, S. / Whitlow, M. #2: Journal: Bioorg.Med.Chem.Lett. / Year: 2007 Title: 3-Mercaptopropionic acids as efficacious inhibitors of activated thrombin activatable fibrinolysis inhibitor (TAFIa). Authors: Islam, I. / Bryant, J. / May, K. / Mohan, R. / Yuan, S. / Kent, L. / Morser, J. / Zhao, L. / Vergona, R. / White, K. / Adler, M. / Whitlow, M. / Buckman, B.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pj4.cif.gz | 140.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pj4.ent.gz | 109.3 KB | Display | PDB format |
PDBx/mmJSON format | 2pj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pj/2pj4 ftp://data.pdbj.org/pub/pdb/validation_reports/pj/2pj4 | HTTPS FTP |
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-Related structure data
Related structure data | 2piyC 2pizC 2pj0C 2pj1C 2pj2C 2pj3C 2pj5C 2pj6C 2pj7C 2pj8C 2pj9C 2pjaC 2pjbC 2pjcC 1z5rS 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
#1: Protein | Mass: 34739.859 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P09955, carboxypeptidase B #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: 2.53 Å3/Da / Density % sol: 51.46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: SODIUM CHLORIDE, TRIS, SODIUM CACODYLATE, PEG 8000, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 9, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 49034 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.66 % / Biso Wilson estimate: 10.8 Å2 / Rsym value: 0.1428 / Net I/σ(I): 9.28 |
Reflection shell | Resolution: 2→2.12 Å / Redundancy: 6.83 % / Mean I/σ(I) obs: 2.18 / Rsym value: 0.3807 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Z5R Resolution: 2→23.92 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 132154.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.72 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→23.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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