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Yorodumi- PDB-1apu: Crystallographic analysis of a pepstatin analogue binding to the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1apu | ||||||
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Title | Crystallographic analysis of a pepstatin analogue binding to the aspartyl proteinase penicillopepsin at 1.8 angstroms resolution | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / ACID PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information penicillopepsin / aspartic-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | Penicillium janthinellum (fungus) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Sielecki, A.R. / James, M.N.G. | ||||||
Citation | Journal: Biochemistry / Year: 1992 Title: Crystallographic Analysis of Transition State Mimics Bound to Penicillopepsin: Difluorostatine-and Difluorostatone-Containing Peptides Authors: James, M.N.G. / Sielecki, A.R. / Moult, J. #1: Journal: Peptides: Structure and Function, Proceedings of the of the Eighth American Peptide Symposium Year: 1983 Title: Crystallographic Analysis of a Pepstatin Analogue Binding to the Aspartyl Proteinase Penicillopepsin at 1.8 Angstroms Resolution Authors: James, M.N.G. / Sielecki, A.R. / Hayakawa, K. / Gelb, M.H. #2: Journal: Biological Macromolecules and Assemblies / Year: 1987 Title: Aspartic Proteinases and Their Catalytic Pathway Authors: James, M.N.G. / Sielecki, A.R. #3: Journal: Biochemistry / Year: 1985 Title: Stereochemical Analysis of Peptide Bond Hydrolysis Catalyzed by the Aspartic Proteinase Penicillopepsin Authors: James, M.N.G. / Sielecki, A.R. #4: Journal: Aspartic Proteinases and Their Inhibitors / Year: 1985 Title: X-Ray Diffraction Studies on Penicillopepsin and its Complexes: The Hydrolytic Mechanism Authors: James, M.N.G. / Sielecki, A.R. / Hofmann, T. #5: Journal: Biochemistry / Year: 1984 Title: Effect of Ph on the Activities of Penicillopepsin and Rhizopus Pepsin and a Proposal for the Productive Substrate Binding Mode in Penicillopepsin Authors: Hofmann, T. / Hodges, R.S. / James, M.N.G. #6: Journal: J.Mol.Biol. / Year: 1983 Title: Structure and Refinement of Penicillopepsin at 1.8 Angstroms Resolution Authors: James, M.N.G. / Sielecki, A.R. #7: Journal: Proc.Natl.Acad.Sci.USA / Year: 1982 Title: Conformational Flexibility in the Active Sites of Aspartyl Proteinases Revealed by a Pepstatin Fragment Binding to Penicillopepsin Authors: James, M.N.G. / Sielecki, A. / Salituro, F. / Rich, D.H. / Hofmann, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1apu.cif.gz | 77.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1apu.ent.gz | 59.7 KB | Display | PDB format |
PDBx/mmJSON format | 1apu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1apu_validation.pdf.gz | 393.3 KB | Display | wwPDB validaton report |
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Full document | 1apu_full_validation.pdf.gz | 395.8 KB | Display | |
Data in XML | 1apu_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 1apu_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/1apu ftp://data.pdbj.org/pub/pdb/validation_reports/ap/1apu | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Atom site foot note | 1: RESIDUES PRO E 134 AND PRO E 315 ARE CIS PROLINES. 2: THE REGION FROM SER E 277 TO SER E 281 IS POORLY ORDERED. | |||||||||||||||
Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33468.809 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Penicillium janthinellum (fungus) / References: UniProt: P00798, penicillopepsin |
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#2: Protein/peptide | |
#3: Sugar | ChemComp-MAN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.74 % |
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.8→8 Å / σ(I): 1 /
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Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
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Refine LS restraints |
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