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Yorodumi- PDB-6f1n: Estimation of relative drug-target residence times by random acce... -
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-Basic information
Entry | Database: PDB / ID: 6f1n | ||||||
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Title | Estimation of relative drug-target residence times by random acceleration molecular dynamics simulation | ||||||
Components | Heat shock protein HSP 90-alpha | ||||||
Keywords | CHAPERONE / CHAPERONE PROTEIN / ATP BINDING | ||||||
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 / Resolution: 2.09 Å | ||||||
Authors | Musil, D. / Lehmann, M. / Eggenweiler, H.-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 | 6f1n.cif.gz | 100.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f1n.ent.gz | 77.1 KB | Display | PDB format |
PDBx/mmJSON format | 6f1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6f1n_validation.pdf.gz | 800.6 KB | Display | wwPDB validaton report |
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Full document | 6f1n_full_validation.pdf.gz | 801.7 KB | Display | |
Data in XML | 6f1n_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 6f1n_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/6f1n ftp://data.pdbj.org/pub/pdb/validation_reports/f1/6f1n | HTTPS FTP |
-Related structure data
Related structure data | 5lo5C 5lo6C 6ei5C 6el5C 6elnC 6eloC 6elpC 6ey8C 6ey9C 6eyaC 6eybC 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: 26601.773 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-SO4 / |
#3: Chemical | ChemComp-C8W / |
#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: 3.13 Å3/Da / Density % sol: 60.76 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Na-cacodylate, pH 6.5 30% PEG8000 0.2 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 8, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→50 Å / Num. obs: 14942 / % possible obs: 84.2 % / Redundancy: 4.5 % / Biso Wilson estimate: 42.76 Å2 / Rmerge(I) obs: 0.05 / Χ2: 1.125 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 2.09→2.18 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.239 / Num. unique obs: 522 / Χ2: 0.895 / % possible all: 30 |
-Processing
Software |
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Refinement | Resolution: 2.09→45.06 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.946 / SU R Cruickshank DPI: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.207 / SU Rfree Blow DPI: 0.163 / SU Rfree Cruickshank DPI: 0.162
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Displacement parameters | Biso max: 162.67 Å2 / Biso mean: 62.54 Å2 / Biso min: 31.59 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.09→45.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.09→2.23 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
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Refinement TLS params. | Method: refined / Origin x: 65.1076 Å / Origin y: 30.2461 Å / Origin z: 29.0075 Å
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Refinement TLS group | Selection details: { A|* } |