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- PDB-1fq6: X-RAY STRUCTURE OF GLYCOL INHIBITOR PD-133,450 BOUND TO SACCHAROPEPSIN -
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Open data
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Basic information
Entry | Database: PDB / ID: 1fq6 | |||||||||
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Title | X-RAY STRUCTURE OF GLYCOL INHIBITOR PD-133,450 BOUND TO SACCHAROPEPSIN | |||||||||
![]() | SACCHAROPEPSIN | |||||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | 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. | |||||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.8 KB | Display | ![]() |
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PDB format | ![]() | 62.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() ![]() |
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#2: Polysaccharide | alpha-L-gulopyranose-(1-2)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-L-gulopyranose-(1-2)-beta-D-mannopyranose-(1-3)-beta-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: Chemical | ChemComp-0QF / ![]() References: N-[(1S)-2-{[(2S,3R,4S)-1-cyclohexyl-3,4-dihydroxy-6-methylheptan-2-yl]amino}-1-(ethylsulfanyl)-2-oxoethyl]-Nalpha-(morpholin-4-ylsulfonyl)-L-phenylalaninamide |
#4: Sugar | ChemComp-NAG / |
#5: Water | ChemComp-HOH / |
Nonpolymer details | DIOL MOIETY SPANNING P1-P1' INHIBITOR SITES (ACDMH - (2S,3R,4S) 2-AMINO-1CYCLOHEXYL-3,4-DIHYDROXY-6- ...DIOL MOIETY SPANNING P1-P1' INHIBITOR SITES (ACDMH - (2S,3R,4S) 2-AMINO-1CYCLOHEXYL |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.37 % | ||||||||||||||||||||||||
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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: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→15.6 Å / Num. all: 19352 / Num. obs: 12831 / % possible obs: 93.7 % / Observed criterion σ(I): 3 / Redundancy: 5 % / Rmerge(I) obs: 0.15 |
Reflection | *PLUS Redundancy: 4.9 % / Num. measured all: 63513 / Rmerge(I) obs: 0.154 |
Reflection shell | *PLUS % possible obs: 71.1 % / Rmerge(I) obs: 0.812 |
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Processing
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Refinement | Resolution: 2.7→15.6 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.7→15.6 Å
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Software | *PLUS Name: RESTRAIN / Classification: refinement | |||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 15.6 Å / σ(F): 0 / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.18 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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