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- PDB-2piz: CRYSTAL STRUCTURE OF ACTIVATED PORCINE PANCREATIC CARBOXYPEPTIDAS... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2piz | ||||||
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Title | CRYSTAL STRUCTURE OF ACTIVATED PORCINE PANCREATIC CARBOXYPEPTIDASE B 2-(3-Guanidino-phenyl)-3-[hydroxy-(3-phenyl-propyl)-phosphinoyl]-propionic acid COMPLEX | ||||||
![]() | Carboxypeptidase B | ||||||
![]() | HYDROLASE / CARBOXYPEPTIDASE B / EXOPEPTIDASE / Phosphinate BASED INHIBITORS | ||||||
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 | ![]() | 204.2 KB | Display | ![]() |
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PDB format | ![]() | 162.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 40.3 KB | Display | |
Data in CIF | ![]() | 58 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2piyC ![]() 2pj0C ![]() 2pj1C ![]() 2pj2C ![]() 2pj3C ![]() 2pj4C ![]() 2pj5C ![]() 2pj6C ![]() 2pj7C ![]() 2pj8C ![]() 2pj9C ![]() 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34739.859 Da / Num. of mol.: 3 / Fragment: CATALYTIC DOMAIN / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.05 % |
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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, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 7, 2000 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 112304 / % possible obs: 92.7 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 20.6 Å2 / Rsym value: 0.066 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.398 / % possible all: 92.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1Z5R Resolution: 1.6→8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2230971.34 / 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: 60.94 Å2 / ksol: 0.42 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.66 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
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Xplor file |
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