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Yorodumi- PDB-4est: CRYSTAL STRUCTURE OF THE COVALENT COMPLEX FORMED BY A PEPTIDYL AL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4est | |||||||||
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Title | CRYSTAL STRUCTURE OF THE COVALENT COMPLEX FORMED BY A PEPTIDYL ALPHA,ALPHA-DIFLUORO-BETA-KETO AMIDE WITH PORCINE PANCREATIC ELASTASE AT 1.78-ANGSTROMS RESOLUTION | |||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | |||||||||
Function / homology | Function and homology information pancreatic elastase / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.78 Å | |||||||||
Authors | Takahashi, L.H. / Radhakrishnan, R. / Rosenfieldjunior, R.E. / Meyerjunior, E.F. / Trainor, D.A. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 1989 Title: Crystal Structure of the Covalent Complex Formed by a Peptidyl Alpha,Alpha-Difluoro-Beta-Keto Amide with Porcine Pancreatic Elastase at 1.78-Angstroms Resolution Authors: Takahashi, L.H. / Radhakrishnan, R. / Rosenfieldjunior, R.E. / Meyerjunior, E.F. / Trainor, D.A. #1: Journal: Acta Crystallogr.,Sect.B / Year: 1988 Title: Structure of Native Porcine Pancreatic Elastase at 1.65 Angstroms Resolution Authors: Meyer, E. / Cole, G. / Radhakrishnan, R. / Epp, O. | |||||||||
History |
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Remark 700 | SHEET THE TWO SEVEN STRANDED SHEETS IN THIS STRUCTURE ARE REALLY SIX STRANDED BETA BARRELS. THIS IS ...SHEET THE TWO SEVEN STRANDED SHEETS IN THIS STRUCTURE ARE REALLY SIX STRANDED BETA BARRELS. THIS IS DENOTED BY THE FIRST STRAND RECURRING AS THE LAST STRAND. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4est.cif.gz | 59.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4est.ent.gz | 46.3 KB | Display | PDB format |
PDBx/mmJSON format | 4est.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/4est ftp://data.pdbj.org/pub/pdb/validation_reports/es/4est | 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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Atom site foot note | 1: ATOM OG OF SER E 195 OF THE ENZYME IS COVALENTLY BONDED TO THE CARBONYL CARBON ATOM OF VAI I 4 OF THE INHIBITOR. |
-Components
#1: Protein | Mass: 25928.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Tissue: PANCREAS / References: UniProt: P00772, pancreatic elastase |
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#2: Protein/peptide | |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.25 % |
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Crystal grow | *PLUS pH: 5 / Method: vapor diffusion |
-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.78 Å / Num. obs: 16151 / % possible obs: 71 % / Observed criterion σ(I): 1 / Num. measured all: 36367 / Rmerge(I) obs: 0.087 |
-Processing
Software | Name: EREF / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.78→7 Å / Rfactor Rwork: 0.16 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.78→7 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.78 Å / Lowest resolution: 7 Å / Num. reflection obs: 16151 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: o_angle_d / Dev ideal: 2.28 |