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- PDB-2pj9: CRYSTAL STRUCTURE OF ACTIVATED PORCINE PANCREATIC CARBOXYPEPTIDAS... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2pj9 | ||||||
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Title | CRYSTAL STRUCTURE OF ACTIVATED PORCINE PANCREATIC CARBOXYPEPTIDASE B 2-(3-Aminomethyl-phenyl)-3-{[(R)-1-(benzo[1,2,5]thiadiazole-4-sulfonylamino)-2-methyl-propyl]-hydroxy-phosphinoyl}-propionic acid COMPLEX | ||||||
![]() | Carboxypeptidase B | ||||||
![]() | HYDROLASE / CARBOXYPEPTIDASE B / EXOPEPTIDASE / Phosphinate BASED INHIBITOR | ||||||
Function / homology | ![]() carboxypeptidase B / metallocarboxypeptidase activity / cytoplasmic vesicle / proteolysis / extracellular space / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Adler, M. / Whitlow, M. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.2 KB | Display | ![]() |
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PDB format | ![]() | 58.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 784.4 KB | Display | ![]() |
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Full document | ![]() | 788.1 KB | Display | |
Data in XML | ![]() | 15.5 KB | Display | |
Data in CIF | ![]() | 22.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2piyC ![]() 2pizC ![]() 2pj0C ![]() 2pj1C ![]() 2pj2C ![]() 2pj3C ![]() 2pj4C ![]() 2pj5C ![]() 2pj6C ![]() 2pj7C ![]() 2pj8C ![]() 2pjaC ![]() 2pjbC ![]() 2pjcC ![]() 1z5rS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34739.859 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-281 / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.42 % |
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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: 93.2 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 11, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→50 Å / Num. obs: 54267 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 3.14 % / Biso Wilson estimate: 19.9 Å2 / Rsym value: 0.0673 / Net I/σ(I): 24.43 |
Reflection shell | Resolution: 1.44→1.53 Å / Redundancy: 2.29 % / Mean I/σ(I) obs: 2.25 / Rsym value: 0.3417 / % possible all: 90.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1Z5R Resolution: 1.56→24.11 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 168189.35 / 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: 54.68 Å2 / ksol: 0.37 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.56→24.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.56→1.62 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 10
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Xplor file |
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