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Yorodumi- PDB-1ppm: CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION-STATE MIMICS BOUND TO PEN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ppm | ||||||
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Title | CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION-STATE MIMICS BOUND TO PENICILLOPEPSIN: PHOSPHORUS-CONTAINING PEPTIDE ANALOGUES | ||||||
Components | PENICILLOPEPSIN | ||||||
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: 1.7 Å | ||||||
Authors | Fraser, M.E. / James, M.N.G. | ||||||
Citation | Journal: Biochemistry / Year: 1992 Title: Crystallographic analysis of transition-state mimics bound to penicillopepsin: phosphorus-containing peptide analogues. Authors: Fraser, M.E. / Strynadka, N.C. / Bartlett, P.A. / Hanson, J.E. / James, M.N. #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: J.Mol.Biol. / Year: 1983 Title: Structure and Refinement of Penicillopepsin at 1.8 Angstroms Resolution Authors: James, M.N.G. / Sielecki, A.R. #4: 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. #5: Journal: STRUCTURAL STUDIES ON MOLECULES OF BIOLOGICA INTERESTL Year: 1981 Title: The Tertiary Structure of Penicillopepsin. Towards a Catalytic Mechanism for Acid Proteases Authors: James, M.N.G. / Hsu, I-N. / Hofmann, T. / Sielecki, A.R. #6: Journal: Can.J.Biochem. / Year: 1980 Title: An X-Ray Crystallographic Approach to Enzyme Structure and Function Authors: James, M.N.G. #7: Journal: Nature / Year: 1978 Title: Structural Evidence for Gene Duplication in the Evolution of the Acid Proteases Authors: Tang, J. / James, M.N.G. / Hsu, I.N. / Jenkins, J.A. / Blundell, T.L. #8: Journal: Nature / Year: 1977 Title: Mechanism of Acid Protease Catalysis Based on the Crystal Structure of Penicillopepsin Authors: James, M.N.G. / Hsu, I.-N. / Delbaere, L.T.J. #9: Journal: Nature / Year: 1977 Title: Penicillopepsin from Penicillium Janthinellum Crystal Structure at 2.8 Angstroms and Sequence Homology with Porcine Pepsin Authors: Hsu, I.-N. / Delbaere, L.T.J. / James, M.N.G. / Hofmann, T. #10: Journal: Adv.Exp.Med.Biol. / Year: 1977 Title: Penicillopepsin. 2.8 Angstroms Structure, Active Site Conformation and Mechanistic Implications Authors: Hsu, I-N. / Delbaere, L.T.J. / James, M.N.G. / Hofmann, T. #11: Journal: Biochem.Biophys.Res.Commun. / Year: 1976 Title: The Crystal Structure of Penicillopepsin at 6 Angstroms Resolution Authors: Hsu, I-N. / Hofmann, T. / Nyburg, S.C. / James, M.N.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ppm.cif.gz | 77.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ppm.ent.gz | 59.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ppm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ppm_validation.pdf.gz | 494.4 KB | Display | wwPDB validaton report |
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Full document | 1ppm_full_validation.pdf.gz | 502.6 KB | Display | |
Data in XML | 1ppm_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 1ppm_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pp/1ppm ftp://data.pdbj.org/pub/pdb/validation_reports/pp/1ppm | 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 134 AND 315 ARE CIS PROLINES. | ||||||||
Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules E
#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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-Sugars , 2 types, 2 molecules
#3: Sugar | ChemComp-MAN / |
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#4: Sugar | ChemComp-ARA / |
-Non-polymers , 3 types, 308 molecules
#2: Chemical | ChemComp-0P1 / |
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#5: Chemical | ChemComp-SO4 / |
#6: Water | ChemComp-HOH / |
-Details
Nonpolymer details | XYS IS POORLY DEFINED IN THE ELECTRON DENSITY |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.19 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 18-22 ℃ / pH: 4.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
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: 1.7 Å / Lowest resolution: 60 Å / Num. all: 29687 / Num. obs: 26564 / Num. measured all: 100309 / Rmerge(I) obs: 0.055 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.15 / Rfactor obs: 0.15 / Highest resolution: 1.7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.7 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 8 Å / Num. reflection obs: 25614 / Rfactor obs: 0.15 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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