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- PDB-1dpj: THE STRUCTURE OF PROTEINASE A COMPLEXED WITH IA3 PEPTIDE INHIBITOR -
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Open data
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Basic information
Entry | Database: PDB / ID: 1dpj | |||||||||
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Title | THE STRUCTURE OF PROTEINASE A COMPLEXED WITH IA3 PEPTIDE INHIBITOR | |||||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / proteinase A / IA3 peptide / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | |||||||||
Function / homology | ![]() saccharopepsin / protein catabolic process in the vacuole / microautophagy / cytoplasm to vacuole targeting by the Cvt pathway / oligosaccharide binding / pexophagy / aspartic-type endopeptidase inhibitor activity / negative regulation of endopeptidase activity / fungal-type vacuole / vacuole ...saccharopepsin / protein catabolic process in the vacuole / microautophagy / cytoplasm to vacuole targeting by the Cvt pathway / oligosaccharide binding / pexophagy / aspartic-type endopeptidase inhibitor activity / negative regulation of endopeptidase activity / fungal-type vacuole / vacuole / endopeptidase inhibitor activity / proteolysis involved in protein catabolic process / macroautophagy / autophagy / disordered domain specific binding / peptidase activity / protease binding / aspartic-type endopeptidase activity / endoplasmic reticulum / protein-containing complex / mitochondrion / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Li, M. / Phylip, H.L. / Lees, W.E. / Winther, J.R. / Dunn, B.M. / Wlodawer, A. / Kay, J. / Guschina, A. | |||||||||
![]() | ![]() Title: The aspartic proteinase from Saccharomyces cerevisiae folds its own inhibitor into a helix. Authors: Li, M. / Phylip, L.H. / Lees, W.E. / Winther, J.R. / Dunn, B.M. / Wlodawer, A. / Kay, J. / Gustchina, A. #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 | ![]() | 92.4 KB | Display | ![]() |
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PDB format | ![]() | 73.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 878.5 KB | Display | ![]() |
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Full document | ![]() | 882.3 KB | Display | |
Data in XML | ![]() | 19.9 KB | Display | |
Data in CIF | ![]() | 30 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 35774.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein/peptide | Mass: 3692.155 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() |
-Sugars , 2 types, 2 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-2)-alpha-D- ...beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 376 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE RESIDUE NUMBERS FOR CHAIN A FOLLOW THE RESIDUE NUMBERS IN PDB ENTRY 2JXR. THE SEQUENCE FOR ...THE RESIDUE NUMBERS FOR CHAIN A FOLLOW THE RESIDUE NUMBERS IN PDB ENTRY 2JXR. THE SEQUENCE FOR CHAIN B IS TRUNCATED. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64.82 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 1500, Ammounia Sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.6 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM / Detector: CCD / Date: Sep 3, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→30 Å / Num. all: 53659 / Num. obs: 53659 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 24 |
Reflection shell | Resolution: 1.78→1.84 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.71 / Num. unique all: 5236 / % possible all: 98.4 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 99.1 % / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 2.5 |
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Processing
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Refinement | Resolution: 1.8→30 Å / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 30 Å / σ(F): 0 / Rfactor obs: 0.2055 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.8 |