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Yorodumi- PDB-1apw: CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION STATE MIMICS BOUND TO PEN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1apw | |||||||||
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Title | CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION STATE MIMICS BOUND TO PENICILLOPEPSIN: DIFLUOROSTATINE-AND DIFLUOROSTATONE-CONTAINING PEPTIDES | |||||||||
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. / Sielecki, A.R. / Hayakawa, K. / Gelb, M.H. #1: Journal: Biological Macromolecules and Assemblies / Year: 1987 Title: Aspartic Proteinases and Their Catalytic Pathway Authors: James, M.N.G. / Sielecki, A.R. #2: 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. #3: 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. #4: 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. #5: 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. / Moult, J. #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 | 1apw.cif.gz | 77.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1apw.ent.gz | 59.5 KB | Display | PDB format |
PDBx/mmJSON format | 1apw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1apw_validation.pdf.gz | 429.9 KB | Display | wwPDB validaton report |
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Full document | 1apw_full_validation.pdf.gz | 434.2 KB | Display | |
Data in XML | 1apw_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 1apw_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/1apw ftp://data.pdbj.org/pub/pdb/validation_reports/ap/1apw | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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. 3: THE FOLLOWING WATER MOLECULES ARE SITTING ON A SPECIAL POSITION: HOH 563, HOH 584 AND HOH 585. | ||||||||||||
Components on special symmetry positions |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules EI
#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 | Mass: 506.626 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: TRANSITION STATE MIMIC |
-Sugars , 2 types, 2 molecules
#3: Sugar | ChemComp-MAN / |
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#4: Sugar | ChemComp-HSY / |
-Non-polymers , 3 types, 297 molecules
#5: Chemical | ChemComp-SO4 / |
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#6: Chemical | ChemComp-DMF / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.37 % |
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Crystal grow | *PLUS Method: other / Details: NMR |
-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 45 Å / Num. all: 27895 / Num. obs: 24987 / Rmerge(I) obs: 0.031 |
-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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Software | *PLUS Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 8 Å / Num. reflection obs: 22464 / σ(I): 1 / Rfactor obs: 0.131 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 12.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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