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Yorodumi- PDB-1fq5: X-ray structure of a cyclic statine inhibitor PD-129,541 bound to... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fq5 | |||||||||
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Title | X-ray structure of a cyclic statine inhibitor PD-129,541 bound to yeast proteinase A | |||||||||
Components | SACCHAROPEPSIN | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
Function / homology | Function and homology information saccharopepsin / microautophagy / cytoplasm to vacuole targeting by the Cvt pathway / oligosaccharide binding / pexophagy / fungal-type vacuole / proteolysis involved in protein catabolic process / macroautophagy / autophagy / disordered domain specific binding ...saccharopepsin / microautophagy / cytoplasm to vacuole targeting by the Cvt pathway / oligosaccharide binding / pexophagy / fungal-type vacuole / proteolysis involved in protein catabolic process / macroautophagy / autophagy / disordered domain specific binding / peptidase activity / aspartic-type endopeptidase activity / endoplasmic reticulum / protein-containing complex / mitochondrion Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å | |||||||||
Authors | Cronin, N.B. / Badasso, M.O. / Tickle, I.J. / Dreyer, T. / Hoover, D.J. / Rosati, R.L. / Humblet, C.C. / Lunney, E.A. / Cooper, J.B. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: X-ray structures of five renin inhibitors bound to saccharopepsin: exploration of active-site specificity. Authors: Cronin, N.B. / Badasso, M.O. / J Tickle, I. / Dreyer, T. / Hoover, D.J. / Rosati, R.L. / Humblet, C.C. / Lunney, E.A. / Cooper, J.B. #1: Journal: J.Mol.Biol. / Year: 1997 Title: The Three-dimensional Structure at 2.4 A Resolution of Glycosylated Proteinase A from the Lysosome-like Vacuole of Saccharomyces cerevisiae Authors: Aguilar, C.F. / Cronin, N.B. / Badasso, M. / Dreyer, T. / Newman, M.P. / Cooper, J.B. / Hoover, D.J. / Wood, S.P. / Johnson, M.S. / Blundell, T.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fq5.cif.gz | 80.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fq5.ent.gz | 63.1 KB | Display | PDB format |
PDBx/mmJSON format | 1fq5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fq5_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1fq5_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1fq5_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | 1fq5_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/1fq5 ftp://data.pdbj.org/pub/pdb/validation_reports/fq/1fq5 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35774.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07267, saccharopepsin |
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#2: Polysaccharide | beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Sugar | ChemComp-NAG / |
#4: Chemical | ChemComp-0GM / |
#5: Water | ChemComp-HOH / |
Nonpolymer details | CYCLIC PEPTIDO-MIMETIC STATIN INHIBITOR PD-129,541 WITH KI IN NANOMOLAR RANGE. THE AUTHORS CALL THE ...CYCLIC PEPTIDO-MIMETIC STATIN INHIBITOR PD-129,541 WITH KI IN NANOMOLAR RANGE. THE AUTHORS CALL THE INHIBITOR CYCLIC STATINE INHIBITOR PD-129,541, BNMA(BIS-[(1-NAPHTHYL)METHYL]ACETIC ACID)-GLU-STATINE-LEU-AMPMA(META-DI(AMINOMETHY |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63.85 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 6000, Sodium Acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 56 % | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1.01 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.01 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→12.9 Å / Num. all: 25823 / Num. obs: 17302 / % possible obs: 89.6 % / Observed criterion σ(I): 3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.07 |
Reflection | *PLUS Num. measured all: 50021 / Rmerge(I) obs: 0.071 |
Reflection shell | *PLUS % possible obs: 81.2 % / Rmerge(I) obs: 0.641 |
-Processing
Software |
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Refinement | Resolution: 2.4→12.9 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→12.9 Å
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Software | *PLUS Name: RESTRAIN / Classification: refinement | |||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 12.9 Å / Num. reflection all: 0 / σ(F): 0 / Rfactor obs: 0.2 / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.2 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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