+Open data
-Basic information
Entry | Database: PDB / ID: 7d26 | ||||||
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Title | Hsp90 alpha N-terminal domain in complex with a 8 compund | ||||||
Components | Heat shock protein HSP 90-alpha | ||||||
Keywords | CHAPERONE/INHIBITOR / CHAPERONE-Inhibitor complex | ||||||
Function / homology | Function and homology information Drug-mediated inhibition of ERBB2 signaling / ESR-mediated signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / HSF1-dependent transactivation / Signaling by ERBB2 / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / HSF1 activation / RHOBTB2 GTPase cycle / Sema3A PAK dependent Axon repulsion ...Drug-mediated inhibition of ERBB2 signaling / ESR-mediated signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / HSF1-dependent transactivation / Signaling by ERBB2 / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / HSF1 activation / RHOBTB2 GTPase cycle / Sema3A PAK dependent Axon repulsion / Downregulation of ERBB2 signaling / Attenuation phase / Regulation of necroptotic cell death / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / VEGFR2 mediated vascular permeability / positive regulation of cytotoxic T cell differentiation / Extra-nuclear estrogen signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of actin dynamics for phagocytic cup formation / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition / Estrogen-dependent gene expression / VEGFA-VEGFR2 Pathway / sperm mitochondrial sheath / dATP binding / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / UTP binding / sperm plasma membrane / telomerase holoenzyme complex assembly / protein insertion into mitochondrial outer membrane / Rho GDP-dissociation inhibitor binding / TPR domain binding / non-chaperonin molecular chaperone ATPase / dendritic growth cone / regulation of postsynaptic membrane neurotransmitter receptor levels / regulation of protein ubiquitination / skeletal muscle contraction / telomere maintenance via telomerase / positive regulation of cell size / response to unfolded protein / chaperone-mediated protein complex assembly / sperm flagellum / axonal growth cone / positive regulation of lamellipodium assembly / DNA polymerase binding / positive regulation of defense response to virus by host / cardiac muscle cell apoptotic process / protein folding chaperone / response to salt stress / positive regulation of cardiac muscle contraction / nitric oxide biosynthetic process / activation of innate immune response / nitric-oxide synthase regulator activity / positive regulation of interferon-beta production / Neutrophil degranulation / response to cold / protein tyrosine kinase binding / response to cocaine / brush border membrane / ATP-dependent protein folding chaperone / neuron migration / tau protein binding / cellular response to virus / histone deacetylase binding / positive regulation of protein import into nucleus / response to estrogen / positive regulation of protein catabolic process / regulation of protein localization / disordered domain specific binding / positive regulation of nitric oxide biosynthetic process / unfolded protein binding / melanosome / protein folding / GTPase binding / myelin sheath / cellular response to heat / protein refolding / response to heat / scaffold protein binding / basolateral plasma membrane / protein phosphatase binding / collagen-containing extracellular matrix / regulation of apoptotic process / transmembrane transporter binding / protein stabilization / response to xenobiotic stimulus / positive regulation of protein phosphorylation / apical plasma membrane / response to antibiotic / mRNA binding / neuronal cell body / ubiquitin protein ligase binding / GTP binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Shin, S.C. / Kim, E.E. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Int J Mol Sci / Year: 2020 Title: Structural Basis for Design of New Purine-Based Inhibitors Targeting the Hydrophobic Binding Pocket of Hsp90. Authors: Shin, S.C. / El-Damasy, A.K. / Lee, J.H. / Seo, S.H. / Kim, J.H. / Seo, Y.H. / Lee, Y. / Yu, J.H. / Bang, E.K. / Kim, E.E. / Keum, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d26.cif.gz | 62 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d26.ent.gz | 42.4 KB | Display | PDB format |
PDBx/mmJSON format | 7d26.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/7d26 ftp://data.pdbj.org/pub/pdb/validation_reports/d2/7d26 | HTTPS FTP |
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-Related structure data
Related structure data | 7d1vC 7d22C 7d24C 7d25C 5h22S S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 24109.275 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hsp90aa1, Hsp86, Hsp86-1, Hspca / Production host: Escherichia coli (E. coli) / References: UniProt: P07901 |
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#2: Chemical | ChemComp-GQ9 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.27 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 1.0M ammonium Sulfate, 0.1M Tris-HCl (pH8.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 29, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.748→50 Å / Num. obs: 29933 / % possible obs: 98.6 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.093 / Χ2: 1.607 / Net I/σ(I): 12 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5h22 Resolution: 1.75→30.742 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.49 / Phase error: 21.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.74 Å2 / Biso mean: 29.5646 Å2 / Biso min: 15.39 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.75→30.742 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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