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Yorodumi- PDB-5odx: Crystal Structure of Hsp90-alpha N-Domain in complex with Indazol... -
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-Basic information
Entry | Database: PDB / ID: 5odx | ||||||
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Title | Crystal Structure of Hsp90-alpha N-Domain in complex with Indazole derivative | ||||||
Components | Heat shock protein HSP 90-alpha | ||||||
Keywords | CHAPERONE | ||||||
Function / homology | Function and homology information sperm mitochondrial sheath / dATP binding / Scavenging by Class F Receptors / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / UTP binding / sperm plasma membrane / positive regulation of tau-protein kinase activity ...sperm mitochondrial sheath / dATP binding / Scavenging by Class F Receptors / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / UTP binding / sperm plasma membrane / positive regulation of tau-protein kinase activity / chaperone-mediated autophagy / telomerase holoenzyme complex assembly / protein insertion into mitochondrial outer membrane / Respiratory syncytial virus genome replication / Rho GDP-dissociation inhibitor binding / Uptake and function of diphtheria toxin / mitochondrial transport / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / PIWI-interacting RNA (piRNA) biogenesis / TPR domain binding / non-chaperonin molecular chaperone ATPase / Assembly and release of respiratory syncytial virus (RSV) virions / regulation of postsynaptic membrane neurotransmitter receptor levels / dendritic growth cone / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / skeletal muscle contraction / HSF1-dependent transactivation / positive regulation of cell size / response to unfolded protein / telomere maintenance via telomerase / chaperone-mediated protein complex assembly / protein unfolding / HSF1 activation / regulation of protein-containing complex assembly / Attenuation phase / RHOBTB2 GTPase cycle / eNOS activation / axonal growth cone / positive regulation of lamellipodium assembly / DNA polymerase binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / : / Signaling by ERBB2 / cardiac muscle cell apoptotic process / positive regulation of defense response to virus by host / endocytic vesicle lumen / positive regulation of cardiac muscle contraction / Recruitment of NuMA to mitotic centrosomes / response to salt stress / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / activation of innate immune response / nitric-oxide synthase regulator activity / positive regulation of interferon-beta production / response to cold / Constitutive Signaling by Overexpressed ERBB2 / AURKA Activation by TPX2 / lysosomal lumen / ESR-mediated signaling / protein tyrosine kinase binding / VEGFR2 mediated vascular permeability / response to cocaine / brush border membrane / ATP-dependent protein folding chaperone / Signaling by ERBB2 TMD/JMD mutants / neuron migration / Constitutive Signaling by EGFRvIII / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Signaling by ERBB2 ECD mutants / tau protein binding / Signaling by ERBB2 KD Mutants / Regulation of necroptotic cell death / Regulation of actin dynamics for phagocytic cup formation / cellular response to virus / Downregulation of ERBB2 signaling / VEGFA-VEGFR2 Pathway / histone deacetylase binding / Aggrephagy / positive regulation of protein import into nucleus / Chaperone Mediated Autophagy / response to estrogen / positive regulation of protein catabolic process / The role of GTSE1 in G2/M progression after G2 checkpoint / regulation of protein localization / Regulation of PLK1 Activity at G2/M Transition / positive regulation of nitric oxide biosynthetic process / disordered domain specific binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.82 Å | ||||||
Authors | Amaral, M. / Schuetz, D. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2018 Title: Ligand Desolvation Steers On-Rate and Impacts Drug Residence Time of Heat Shock Protein 90 (Hsp90) Inhibitors. Authors: Schuetz, D.A. / Richter, L. / Amaral, M. / Grandits, M. / Gradler, U. / Musil, D. / Buchstaller, H.P. / Eggenweiler, H.M. / Frech, M. / Ecker, G.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5odx.cif.gz | 103.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5odx.ent.gz | 78.4 KB | Display | PDB format |
PDBx/mmJSON format | 5odx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5odx_validation.pdf.gz | 874.3 KB | Display | wwPDB validaton report |
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Full document | 5odx_full_validation.pdf.gz | 875.8 KB | Display | |
Data in XML | 5odx_validation.xml.gz | 13 KB | Display | |
Data in CIF | 5odx_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/5odx ftp://data.pdbj.org/pub/pdb/validation_reports/od/5odx | HTTPS FTP |
-Related structure data
Related structure data | 5lnyC 5lnzC 5lo0C 5lo1C 5nyhC 5ociC 5od7C 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: 25713.822 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90AA1, HSP90A, HSPC1, HSPCA / Production host: Escherichia coli (E. coli) / References: UniProt: P07900 | ||
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#2: Chemical | ChemComp-9RZ / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.22 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium fluoride, 0.1 M Bis Tris propane, pH 8.5, 20 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.819→48.779 Å / Num. obs: 28017 / % possible obs: 99.8 % / Redundancy: 6.57 % / Biso Wilson estimate: 36.93 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.96 |
-Processing
Software |
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Refinement | Resolution: 1.82→22.17 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.951 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.116 / SU Rfree Blow DPI: 0.106 / SU Rfree Cruickshank DPI: 0.101
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Displacement parameters | Biso mean: 39.49 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.82→22.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.81→1.88 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Origin x: 0.6818 Å / Origin y: 29.585 Å / Origin z: 28.7655 Å
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Refinement TLS group | Selection details: { A|* } |