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Yorodumi- PDB-5fpm: Structure of heat shock-related 70kDA protein 2 with small-molecu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fpm | ||||||
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Title | Structure of heat shock-related 70kDA protein 2 with small-molecule ligand 5-phenyl-1,3,4-oxadiazole-2-thiol (AT809) in an alternate binding site. | ||||||
Components | HEAT SHOCK-RELATED 70KDA PROTEIN 2 | ||||||
Keywords | CHAPERONE / HEAT SHOCK-RELATED PROTEIN / HEAT SHOCK / HSP70 / HSPA2 / PROTEIN-LIGAND COMPLEX / FRAGMENT SCREENING / ALTERNATE BINDING SITE / AT809. | ||||||
Function / homology | Function and homology information CatSper complex / glycolipid binding / synaptonemal complex disassembly / negative regulation of inclusion body assembly / male meiotic nuclear division / synaptonemal complex / meiotic spindle / male meiosis I / chaperone cofactor-dependent protein refolding / spermatid development ...CatSper complex / glycolipid binding / synaptonemal complex disassembly / negative regulation of inclusion body assembly / male meiotic nuclear division / synaptonemal complex / meiotic spindle / male meiosis I / chaperone cofactor-dependent protein refolding / spermatid development / response to unfolded protein / Regulation of HSF1-mediated heat shock response / Attenuation phase / protein folding chaperone / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of G2/M transition of mitotic cell cycle / Meiotic synapsis / response to cold / male germ cell nucleus / ATP-dependent protein folding chaperone / tau protein binding / PKR-mediated signaling / disordered domain specific binding / unfolded protein binding / protein-folding chaperone binding / response to heat / protein refolding / spermatogenesis / blood microparticle / positive regulation of protein phosphorylation / enzyme binding / cell surface / ATP hydrolysis activity / extracellular exosome / ATP binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Jhoti, H. / Ludlow, R.F. / Patel, S. / Saini, H.K. / Tickle, I.J. / Verdonk, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Detection of Secondary Binding Sites in Proteins Using Fragment Screening. Authors: Ludlow, R.F. / Verdonk, M.L. / Saini, H.K. / Tickle, I.J. / Jhoti, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fpm.cif.gz | 318.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fpm.ent.gz | 259.4 KB | Display | PDB format |
PDBx/mmJSON format | 5fpm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fpm_validation.pdf.gz | 422.7 KB | Display | wwPDB validaton report |
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Full document | 5fpm_full_validation.pdf.gz | 424.5 KB | Display | |
Data in XML | 5fpm_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 5fpm_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/5fpm ftp://data.pdbj.org/pub/pdb/validation_reports/fp/5fpm | HTTPS FTP |
-Related structure data
Related structure data | 5fp5C 5fp6C 5fpdSC 5fpeC 5fpnC 5fpoC 5fprC 5fpsC 5fptC 5fpyC C: citing same article (ref.) 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.99999, 0.00174, 0.00515), Vector: |
-Components
#1: Protein | Mass: 42383.000 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: P54652 #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | 5-PHENYL-1,3,4-OXADIAZOLE | Sequence details | 3 EXTRA RESIDUES AT N TERM ARE REMAINS OF HIS TAG AFTER THROMBIN CLEAVAGE. RESIDUES 2-3 DELETED. ...3 EXTRA RESIDUES AT N TERM ARE REMAINS OF HIS TAG AFTER THROMBIN CLEAVAGE. RESIDUES 2-3 DELETED. RESIDUES 386-639 DELETED. | |
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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: 2.3 Å3/Da / Density % sol: 46.14 % / Description: NONE |
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Crystal grow | pH: 8 Details: 1.0M NACL, 0.1M TRIS/HCL PH=8, 20.0% W/V PEG 8000. PROTEIN CONC. = 11MG/ML. |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 |
Detector | Type: RIGAKU SATURN CCD / Detector: CCD / Date: Jun 24, 2008 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→38.4 Å / Num. obs: 53541 / % possible obs: 97.8 % / Observed criterion σ(I): -3.7 / Redundancy: 2.2 % / Biso Wilson estimate: 24.64 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.96→2.03 Å / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2.9 / % possible all: 89.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5FPD Resolution: 1.96→38.37 Å / Cor.coef. Fo:Fc: 0.9491 / Cor.coef. Fo:Fc free: 0.9282 / SU R Cruickshank DPI: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.206 / SU Rfree Blow DPI: 0.166 / SU Rfree Cruickshank DPI: 0.156
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Displacement parameters | Biso mean: 26.63 Å2
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Refine analyze | Luzzati coordinate error obs: 0.191 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→38.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.96→2.01 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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