+Open data
-Basic information
Entry | Database: PDB / ID: 5lo5 | ||||||
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Title | HSP90 WITH indole derivative | ||||||
Components | Heat shock protein HSP 90-alpha | ||||||
Keywords | CHAPERONE | ||||||
Function / homology | Function and homology information 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 / 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 / protein insertion into mitochondrial outer membrane / chaperone-mediated autophagy / telomerase holoenzyme complex assembly / 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 / dendritic growth cone / regulation of postsynaptic membrane neurotransmitter receptor levels / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / skeletal muscle contraction / protein unfolding / telomere maintenance via telomerase / HSF1-dependent transactivation / response to unfolded protein / positive regulation of cell size / chaperone-mediated protein complex assembly / regulation of protein-containing complex assembly / HSF1 activation / Attenuation phase / RHOBTB2 GTPase cycle / positive regulation of defense response to virus by host / eNOS activation / axonal growth cone / positive regulation of lamellipodium assembly / DNA polymerase binding / activation of innate immune response / 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 / response to salt stress / cardiac muscle cell apoptotic process / endocytic vesicle lumen / Recruitment of NuMA to mitotic centrosomes / positive regulation of cardiac muscle contraction / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / nitric-oxide synthase regulator activity / positive regulation of interferon-beta production / response to cold / protein tyrosine kinase binding / lysosomal lumen / AURKA Activation by TPX2 / Constitutive Signaling by Overexpressed ERBB2 / ESR-mediated signaling / VEGFR2 mediated vascular permeability / response to cocaine / ATP-dependent protein folding chaperone / brush border membrane / Signaling by ERBB2 TMD/JMD mutants / neuron migration / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Signaling by ERBB2 KD Mutants / tau protein binding / Regulation of necroptotic cell death / cellular response to virus / Regulation of actin dynamics for phagocytic cup formation / Downregulation of ERBB2 signaling / VEGFA-VEGFR2 Pathway / histone deacetylase binding / positive regulation of protein import into nucleus / Aggrephagy / Chaperone Mediated Autophagy / response to estrogen / positive regulation of protein catabolic process / The role of GTSE1 in G2/M progression after G2 checkpoint / disordered domain specific binding / positive regulation of nitric oxide biosynthetic process / Regulation of PLK1 Activity at G2/M Transition / unfolded protein binding / melanosome Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å | ||||||
Authors | Graedler, U. / Amaral, M. | ||||||
Citation | Journal: J Chem Theory Comput / Year: 2018 Title: Estimation of Drug-Target Residence Times by tau-Random Acceleration Molecular Dynamics Simulations. Authors: Kokh, D.B. / Amaral, M. / Bomke, J. / Gradler, U. / Musil, D. / Buchstaller, H.P. / Dreyer, M.K. / Frech, M. / Lowinski, M. / Vallee, F. / Bianciotto, M. / Rak, A. / Wade, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lo5.cif.gz | 64.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lo5.ent.gz | 45.3 KB | Display | PDB format |
PDBx/mmJSON format | 5lo5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lo5_validation.pdf.gz | 635.2 KB | Display | wwPDB validaton report |
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Full document | 5lo5_full_validation.pdf.gz | 635.6 KB | Display | |
Data in XML | 5lo5_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 5lo5_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/5lo5 ftp://data.pdbj.org/pub/pdb/validation_reports/lo/5lo5 | HTTPS FTP |
-Related structure data
Related structure data | 5lo6C 6ei5C 6el5C 6elnC 6eloC 6elpC 6ey8C 6ey9C 6eyaC 6eybC 6f1nC 4eehS 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: 25713.822 Da / Num. of mol.: 1 / Fragment: ATPASE DOMAIN (8-236) 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-70M / |
#3: Water | ChemComp-HOH / |
Sequence details | HSP90 IN COMPLEX WITH EMD519693 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.22 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M Bis Tris pH 5.5, 0.2 M Ammonium actetate, 25 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X1A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 20, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→70 Å / Num. obs: 55284 / % possible obs: 99.2 % / Redundancy: 5 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 21.52 |
Reflection shell | Resolution: 1.44→1.52 Å / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 2.76 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EEH Resolution: 1.44→70 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.44→70 Å
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