+Open data
-Basic information
Entry | Database: PDB / ID: 3oev | ||||||
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Title | Structure of yeast 20S open-gate proteasome with Compound 25 | ||||||
Components | (Proteasome component ...) x 14 | ||||||
Keywords | Hydrolase/Hydrolase Inhibitor / 20S proteasome / Hydrolase-Hydrolase Inhibitor complex | ||||||
Function / homology | Function and homology information 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 / proteasome storage granule / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / Ub-specific processing proteases ...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 / proteasome storage granule / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / Ub-specific processing proteases / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / Neutrophil degranulation / proteasome complex / proteasomal protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.85 Å | ||||||
Authors | Sintchak, M.D. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2010 Title: Optimization of a series of dipeptides with a P3 threonine residue as non-covalent inhibitors of the chymotrypsin-like activity of the human 20S proteasome. Authors: Blackburn, C. / Barrett, C. / Blank, J.L. / Bruzzese, F.J. / Bump, N. / Dick, L.R. / Fleming, P. / Garcia, K. / Hales, P. / Hu, Z. / Jones, M. / Liu, J.X. / Sappal, D.S. / Sintchak, M.D. / ...Authors: Blackburn, C. / Barrett, C. / Blank, J.L. / Bruzzese, F.J. / Bump, N. / Dick, L.R. / Fleming, P. / Garcia, K. / Hales, P. / Hu, Z. / Jones, M. / Liu, J.X. / Sappal, D.S. / Sintchak, M.D. / Tsu, C. / Gigstad, K.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oev.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3oev.ent.gz | 981.8 KB | Display | PDB format |
PDBx/mmJSON format | 3oev.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/3oev ftp://data.pdbj.org/pub/pdb/validation_reports/oe/3oev | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
-Proteasome component ... , 14 types, 28 molecules AOBPCQDRESFTGUHVIWJXKYLZM1N2
#1: Protein | Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c References: UniProt: P23639, proteasome endopeptidase complex #2: Protein | Mass: 25968.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c References: UniProt: P23638, proteasome endopeptidase complex #3: Protein | Mass: 26903.330 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c References: UniProt: P40303, proteasome endopeptidase complex #4: Protein | Mass: 28649.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c References: UniProt: P32379, proteasome endopeptidase complex #5: Protein | Mass: 25502.805 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c References: UniProt: P40302, proteasome endopeptidase complex #6: Protein | Mass: 26734.328 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c References: UniProt: P21242, proteasome endopeptidase complex #7: Protein | Mass: 27316.037 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c References: UniProt: P21243, proteasome endopeptidase complex #8: Protein | Mass: 23987.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c References: UniProt: P25043, proteasome endopeptidase complex #9: Protein | Mass: 22496.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c References: UniProt: P25451, proteasome endopeptidase complex #10: Protein | Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c References: UniProt: P22141, proteasome endopeptidase complex #11: Protein | Mass: 23325.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c References: UniProt: P30656, proteasome endopeptidase complex #12: Protein | Mass: 24883.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c References: UniProt: P23724, proteasome endopeptidase complex #13: Protein | Mass: 25945.496 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c References: UniProt: P30657, proteasome endopeptidase complex #14: Protein | Mass: 21517.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c References: UniProt: P38624, proteasome endopeptidase complex |
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-Non-polymers , 3 types, 14 molecules
#15: Chemical | ChemComp-MG / #16: Chemical | Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 599.740 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H37N3O5S References: 4-(BENZYLOXY)-N-[(2S,3R)-3-HYDROXY-1-{[(2S)-1-{[(3-METHYLTHIOPHEN-2-YL)METHYL]AMINO}-1-OXO-4-PHENYLBUTAN-2-YL]AMINO}-1-OXOBUTAN-2-YL]BENZAMIDE #17: Chemical | |
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-Details
Nonpolymer details | 3OE IS A NON-COVALENT DI-PEPTIDE SELECTIVE INHIBITOR OF THE HUMAN 20S PROTEASONE |
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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: 3.87 Å3/Da / Density % sol: 68.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 mM MES, pH 7.0, 40 mM MgOAc, 15% 2-methyl-2,4-pentanediol (MPD), 10 mM EDTA, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Type: MAR CCD 165 mm / Detector: CCD | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.85→50 Å / Num. obs: 247646 / % possible obs: 98.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Χ2: 1.051 / Net I/σ(I): 8.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 2.85→50 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.892 / Occupancy max: 1 / Occupancy min: 1 / SU B: 14.419 / SU ML: 0.273 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.663 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 129.11 Å2 / Biso mean: 53.1612 Å2 / Biso min: 26.72 Å2
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Refinement step | Cycle: LAST / Resolution: 2.85→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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