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- PDB-5l64: Yeast 20S proteasome with human beta5c (1-138) and human beta6 (9... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5l64 | ||||||
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Title | Yeast 20S proteasome with human beta5c (1-138) and human beta6 (97-111; 118-133) in complex with epoxyketone inhibitor 18 | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex / ![]() ![]() | ||||||
Function / homology | ![]() proteasome core complex / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Groll, M. / Huber, E.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A humanized yeast proteasome identifies unique binding modes of inhibitors for the immunosubunit beta 5i. Authors: Huber, E.M. / Heinemeyer, W. / de Bruin, G. / Overkleeft, H.S. / Groll, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.4 MB | Display | ![]() |
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PDB format | ![]() | 2 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5l52C ![]() 5l54C ![]() 5l55C ![]() 5l5aC ![]() 5l5bC ![]() 5l5dC ![]() 5l5eC ![]() 5l5fC ![]() 5l5hC ![]() 5l5iC ![]() 5l5jC ![]() 5l5oC ![]() 5l5pC ![]() 5l5qC ![]() 5l5rC ![]() 5l5sC ![]() 5l5tC ![]() 5l5uC ![]() 5l5vC ![]() 5l5wC ![]() 5l5xC ![]() 5l5yC ![]() 5l5zC ![]() 5l60C ![]() 5l61C ![]() 5l62C ![]() 5l63C ![]() 5l65C ![]() 5l66C ![]() 5l67C ![]() 5l68C ![]() 5l69C ![]() 5l6aC ![]() 5l6bC ![]() 5l6cC ![]() 5lttC ![]() 5cz4S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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Components
-Proteasome subunit alpha type- ... , 6 types, 12 molecules AOBPCQDRESGU
#1: Protein | ![]() Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P23639, ![]() #2: Protein | ![]() Mass: 28748.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P23638, ![]() #3: Protein | ![]() Mass: 28478.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P40303, ![]() #4: Protein | ![]() Mass: 28649.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P32379, ![]() #5: Protein | ![]() Mass: 25634.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P40302, ![]() #7: Protein | ![]() Mass: 28033.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P21243, ![]() |
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-Protein , 1 types, 2 molecules FT
#6: Protein | Mass: 31575.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P21242, ![]() |
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-Proteasome subunit beta type- ... , 7 types, 14 molecules HVIWJXKYLZMaNb
#8: Protein | ![]() Mass: 25114.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P25043, ![]() #9: Protein | ![]() Mass: 22627.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P25451, ![]() #10: Protein | ![]() Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P22141, ![]() #11: Protein | ![]() Mass: 23177.207 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() Gene: PSMB5, LMPX, MB1, X, PRE2, DOA3, PRG1, YPR103W, P8283.10 Production host: ![]() ![]() ![]() References: UniProt: P28074, UniProt: P30656, ![]() #12: Protein | ![]() Mass: 24979.010 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Gene: PRE7, PRS3, PTS1, YBL041W, YBL0407, PSMB1, PSC5 Production host: ![]() ![]() ![]() References: UniProt: P23724, UniProt: P20618, ![]() #13: Protein | ![]() Mass: 27200.893 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P30657, ![]() #14: Protein | ![]() Mass: 21517.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() References: UniProt: P38624, ![]() |
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-Non-polymers , 5 types, 449 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/6NV.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/6NV.gif)
![](data/chem/img/HOH.gif)
#15: Chemical | ChemComp-MG / #16: Chemical | ![]() #17: Chemical | ChemComp-MES / ![]() #18: Chemical | #19: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.67 Å3/Da / Density % sol: 66.52 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 20 mM MgAC2, 13% MPD, 0.1 M MES / PH range: 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2015 |
Radiation | Monochromator: LN2 COOLED FIXED-EXIT. SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.7→30 Å / Num. obs: 283074 / % possible obs: 96.3 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 2 / % possible all: 97.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5CZ4 Resolution: 2.7→15 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.934 / SU B: 23.668 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R Free: 0.267 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.59 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→15 Å
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Refine LS restraints |
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