+Open data
-Basic information
Entry | Database: PDB / ID: 3d29 | |||||||||
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Title | Proteasome Inhibition by Fellutamide B | |||||||||
Components |
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Keywords | HYDROLASE / anti-parallel beta-sheet structure flanked by alpha-helices / Cytoplasm / Nucleus / Protease / Proteasome / Threonine protease / Ubl conjugation / Phosphoprotein / Zymogen | |||||||||
Function / homology | Function and homology information proteasome core complex / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 ...proteasome core complex / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / Ub-specific processing proteases / Neutrophil degranulation / proteasome complex / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å | |||||||||
Authors | Groll, M. / Hines, J. / Fahnestock, M. / Crews, M.C. | |||||||||
Citation | Journal: Chem.Biol. / Year: 2008 Title: Proteasome Inhibition by Fellutamide B Induces Nerve Growth Factor Synthesis Authors: Hines, J. / Groll, M. / Fahnestock, M. / Crews, C.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d29.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3d29.ent.gz | 1017.1 KB | Display | PDB format |
PDBx/mmJSON format | 3d29.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d29_validation.pdf.gz | 699.7 KB | Display | wwPDB validaton report |
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Full document | 3d29_full_validation.pdf.gz | 886.2 KB | Display | |
Data in XML | 3d29_validation.xml.gz | 242.2 KB | Display | |
Data in CIF | 3d29_validation.cif.gz | 331 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/3d29 ftp://data.pdbj.org/pub/pdb/validation_reports/d2/3d29 | HTTPS FTP |
-Related structure data
Related structure data | 1rypS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 9 types, 18 molecules AOBPCQDRESFTGUIWLZ
#1: Protein | Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: native purification from cell lysate / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: bakers yeast / References: UniProt: A0A6L1BIF8, UniProt: P23639*PLUS #2: Protein | Mass: 27050.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: native purification from cell lysate / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: bakers yeast / References: UniProt: A0A6A5PXC6, UniProt: P23638*PLUS #3: Protein | Mass: 26903.330 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: native purification from cell lysate / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: bakers yeast / References: UniProt: A0A6A5Q273, UniProt: P40303*PLUS #4: Protein | Mass: 26544.789 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: native purification from cell lysate / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: bakers yeast / References: UniProt: A0A6A5PXN2, UniProt: P32379*PLUS #5: Protein | Mass: 25502.805 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: native purification from cell lysate / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: bakers yeast / References: UniProt: A0A6A5PTH4, UniProt: P40302*PLUS #6: Protein | Mass: 26892.482 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: native purification from cell lysate / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: bakers yeast / References: UniProt: A0A6A5Q4M4, UniProt: P21242*PLUS #7: Protein | Mass: 27316.037 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: native purification from cell lysate / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: bakers yeast / References: UniProt: A0A6A5PYC9, UniProt: P21243*PLUS #9: Protein | Mass: 22496.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: native purification from cell lysate / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: bakers yeast / References: UniProt: A0A6L0YA22, UniProt: P25451*PLUS #12: Protein | Mass: 24883.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: native purification from cell lysate / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: bakers yeast / References: UniProt: A0A6A5Q0P3, UniProt: P23724*PLUS |
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-Proteasome endopeptidase ... , 2 types, 4 molecules HVKY
#8: Protein | Mass: 23987.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: native purification from cell lysate / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: bakers yeast References: UniProt: A0A6A5Q449, UniProt: P25043*PLUS, proteasome endopeptidase complex #11: Protein | Mass: 23325.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: native purification from cell lysate / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: bakers yeast References: UniProt: A0A6A5Q5W3, UniProt: P30656*PLUS, proteasome endopeptidase complex |
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-Proteasome subunit ... , 3 types, 6 molecules JXM1N2
#10: Protein | Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: native purification from cell lysate / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: bakers yeast / References: UniProt: A0A6A5Q0W2, UniProt: P22141*PLUS #13: Protein | Mass: 25945.496 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: native purification from cell lysate / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: bakers yeast / References: UniProt: A0A8H8ULD3, UniProt: P30657*PLUS #14: Protein | Mass: 21517.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: native purification from cell lysate / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: bakers yeast References: UniProt: P38624, proteasome endopeptidase complex |
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-Protein/peptide , 1 types, 6 molecules abcdef
#15: Protein/peptide | Mass: 373.405 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 2 types, 1338 molecules
#16: Chemical | ChemComp-HXD / ( #17: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | THE ALDEHYDE OF FELLUTAMID |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67.67 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 10 % MPD; 0,1 M MES, 30 mM MgAc2, pH 6,8, VAPOR DIFFUSION, HANGING DROP, temperature 298K PH range: 6,8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2006 / Details: DYNAMICALLY BENDABLE MIRROR |
Radiation | Monochromator: LN2 COOLED FIXED-EXIT SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40 Å / Num. all: 331875 / Num. obs: 336246 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 46.3 Å2 / Rmerge(I) obs: 0.066 |
Reflection shell | Resolution: 2.6→2.63 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 2.7 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB Entry 1ryp Resolution: 2.6→15 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3868824.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.9588 Å2 / ksol: 0.365621 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 54 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
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Xplor file |
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