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Yorodumi- PDB-1pph: GEOMETRY OF BINDING OF THE NALPHA-TOSYLATED PIPERIDIDES OF M-AMID... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pph | ||||||
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Title | GEOMETRY OF BINDING OF THE NALPHA-TOSYLATED PIPERIDIDES OF M-AMIDINO-, P-AMIDINO-AND P-GUANIDINO PHENYLALANINE TO THROMBIN AND TRYPSIN: X-RAY CRYSTAL STRUCTURES OF THEIR TRYPSIN COMPLEXES AND MODELING OF THEIR THROMBIN COMPLEXES | ||||||
Components | TRYPSIN | ||||||
Keywords | HYDROLASE/hydrolase inhibitor / SERINE PROTEINASE / HYDROLASE-hydrolase inhibitor complex | ||||||
Function / homology | Function and homology information trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | ||||||
Authors | Bode, W. / Turk, D. | ||||||
Citation | Journal: FEBS Lett. / Year: 1991 Title: Geometry of binding of the N alpha-tosylated piperidides of m-amidino-, p-amidino- and p-guanidino phenylalanine to thrombin and trypsin. X-ray crystal structures of their trypsin complexes ...Title: Geometry of binding of the N alpha-tosylated piperidides of m-amidino-, p-amidino- and p-guanidino phenylalanine to thrombin and trypsin. X-ray crystal structures of their trypsin complexes and modeling of their thrombin complexes. Authors: Turk, D. / Sturzebecher, J. / Bode, W. #1: Journal: Eur.J.Biochem. / Year: 1990 Title: Geometry of Binding of the Benzamidine-and Arginine-Based Inhibitors N Alpha-(2-Naphthyl-Sulphonyl-Glycyl)-Dl-P-Amidinophenylalanyl-Piperidine (Napap) and (2R,4R)-4-Methyl-1-[N Alpha-(3-Methyl- ...Title: Geometry of Binding of the Benzamidine-and Arginine-Based Inhibitors N Alpha-(2-Naphthyl-Sulphonyl-Glycyl)-Dl-P-Amidinophenylalanyl-Piperidine (Napap) and (2R,4R)-4-Methyl-1-[N Alpha-(3-Methyl-1,2,3,4-Tetrahydro-8-Quinolinesulphonyl)-L-Arginyl]-2-Piperidine Carboxylic Acid (Mqpa) to Human Alpha-Thrombin: X-Ray Crystallographic Determination of the Napap-Trypsin Complex and Modeling of Napap-Thrombin and Mqpa-Thrombin Authors: Bode, W. / Turk, D. / Stuerzebecher, J. #2: Journal: Embo J. / Year: 1989 Title: The Refined 1.9 Angstroms Crystal Structure of Human Alpha-Thrombin: Interaction with D-Phe-Pro-Arg Chloromethylketone and Significance of the Tyr-Pro-Pro-Trp Insertion Segment Authors: Bode, W. / Mayr, I. / Baumann, U. / Huber, R. / Stone, S.R. / Hofsteenge, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pph.cif.gz | 56.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pph.ent.gz | 43.4 KB | Display | PDB format |
PDBx/mmJSON format | 1pph.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pp/1pph ftp://data.pdbj.org/pub/pdb/validation_reports/pp/1pph | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Tissue: PANCREAS / References: UniProt: P00760, trypsin |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-0ZG / |
#5: Water | ChemComp-HOH / |
Nonpolymer details | 3-TAPAP, A SYNTHETIC THROMBIN INHIBITOR, IS NONCOVALENTLY BOUND TO THE ACTIVE SITE. A CALCIUM CAL ...3-TAPAP, A SYNTHETIC THROMBIN INHIBITOR, IS NONCOVALEN |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59.06 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 22 ℃ / pH: 6 / Method: vapor diffusion, hanging dropDetails: taken from Bartunik, H.D. et al (1989). J. Mol. Biol., 210, 813-828. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.95 Å / Num. obs: 18614 / Num. measured all: 77873 / Rmerge(I) obs: 0.075 |
-Processing
Software |
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Refinement | Resolution: 1.9→8 Å / Rfactor Rwork: 0.167 / Rfactor obs: 0.167 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 8 Å / Num. reflection obs: 18199 / Rfactor obs: 0.167 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 11.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.43 |