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- PDB-1uy9: Human Hsp90-alpha with 8-Benzo[1,3]dioxol-,5-ylmethyl-9-butyl-9H-... -

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Basic information

Entry
Database: PDB / ID: 1uy9
TitleHuman Hsp90-alpha with 8-Benzo[1,3]dioxol-,5-ylmethyl-9-butyl-9H-purin-6-ylamine
ComponentsHEAT SHOCK PROTEIN HSP 90-ALPHAHeat shock response
KeywordsCHAPERONE / HSP90 / ATPASE / PU6 / ATP-BINDING / HEAT SHOCK
Function / homology
Function and homology information


positive regulation of protein polymerization / protein insertion into mitochondrial outer membrane / telomerase holoenzyme complex assembly / mitochondrial transport / chaperone-mediated autophagy / central nervous system neuron axonogenesis / positive regulation of cellular protein catabolic process / TPR domain binding / dendritic growth cone / chaperone-mediated protein complex assembly ...positive regulation of protein polymerization / protein insertion into mitochondrial outer membrane / telomerase holoenzyme complex assembly / mitochondrial transport / chaperone-mediated autophagy / central nervous system neuron axonogenesis / positive regulation of cellular protein catabolic process / TPR domain binding / dendritic growth cone / chaperone-mediated protein complex assembly / axon extension / regulation of protein ubiquitination / telomere maintenance via telomerase / protein unfolding / regulation of cellular protein localization / DNA polymerase binding / regulation of protein-containing complex assembly / positive regulation of tau-protein kinase activity / MHC class II protein complex binding / go:0051186: / axonal growth cone / protein tyrosine kinase binding / GTPase binding / endocytic vesicle lumen / ciliary basal body-plasma membrane docking / establishment of cell polarity / response to unfolded protein / nitric-oxide synthase regulator activity / positive regulation of telomerase activity / lysosomal lumen / response to cold / regulation of nitric-oxide synthase activity / ERBB2 signaling pathway / tau protein binding / regulation of cellular response to heat / melanosome / regulation of G2/M transition of mitotic cell cycle / histone deacetylase binding / Fc-gamma receptor signaling pathway involved in phagocytosis / vascular endothelial growth factor receptor signaling pathway / cellular response to heat / receptor-mediated endocytosis / unfolded protein binding / G2/M transition of mitotic cell cycle / positive regulation of nitric oxide biosynthetic process / myelin sheath / scaffold protein binding / disordered domain specific binding / response to heat / protein refolding / protein folding / positive regulation of peptidyl-serine phosphorylation / secretory granule lumen / protein stabilization / ficolin-1-rich granule lumen / ATPase activity / positive regulation of protein kinase B signaling / positive regulation of protein phosphorylation / response to antibiotic / cytokine-mediated signaling pathway / neuronal cell body / ubiquitin protein ligase binding / neutrophil degranulation / viral process / perinuclear region of cytoplasm / cell surface / protein homodimerization activity / protein-containing complex / mitochondrion / RNA binding / extracellular exosome / membrane / extracellular region / nucleoplasm / ATP binding / identical protein binding / plasma membrane / nucleus / cytosol / cytoplasm
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / HSP90, C-terminal domain / Histidine kinase/HSP90-like ATPase superfamily / Heat shock protein Hsp90, N-terminal / Ribosomal protein S5 domain 2-type fold / Heat shock protein Hsp90, conserved site / Histidine kinase/HSP90-like ATPase / Heat shock protein Hsp90 family / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 ...Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / HSP90, C-terminal domain / Histidine kinase/HSP90-like ATPase superfamily / Heat shock protein Hsp90, N-terminal / Ribosomal protein S5 domain 2-type fold / Heat shock protein Hsp90, conserved site / Histidine kinase/HSP90-like ATPase / Heat shock protein Hsp90 family / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / 2-Layer Sandwich / Alpha Beta
Heat shock protein HSP 90-alpha
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWright, L. / Barril, X. / Dymock, B. / Sheridan, L. / Surgenor, A. / Beswick, M. / Drysdale, M. / Collier, A. / Massey, A. / Davies, N. / Fink, A. / Fromont, C. / Aherne, W. / Boxall, K. / Sharp, S. / Workman, P. / Hubbard, R.E.
CitationJournal: Chem.Biol. / Year: 2004
Title: Structure-Activity Relationships in Purine-Based Inhibitor Binding to Hsp90 Isoforms
Authors: Wright, L. / Barril, X. / Dymock, B. / Sheridan, L. / Surgenor, A. / Beswick, M. / Drysdale, M. / Collier, A. / Massey, A. / Davies, N. / Fink, A. / Fromont, C. / Aherne, W. / Boxall, K. / ...Authors: Wright, L. / Barril, X. / Dymock, B. / Sheridan, L. / Surgenor, A. / Beswick, M. / Drysdale, M. / Collier, A. / Massey, A. / Davies, N. / Fink, A. / Fromont, C. / Aherne, W. / Boxall, K. / Sharp, S. / Workman, P. / Hubbard, R.E.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 2, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEAT SHOCK PROTEIN HSP 90-ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9272
Polymers26,6021
Non-polymers3251
Water4,936274
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)66.651, 90.806, 98.723
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2018-

HOH

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Components

#1: Protein HEAT SHOCK PROTEIN HSP 90-ALPHA / Heat shock response / HSP 86


Mass: 26601.773 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: MELANOMA / Description: CLONED FROM IMAGE\:4026275 / Organ: SKIN / Plasmid: PET19 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07900
#2: Chemical ChemComp-PU6 / 8-BENZO[1,3]DIOXOL-,5-YLMETHYL-9-BUTYL-9H-


Mass: 325.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N5O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMOLECULAR CHAPERONE HAS ATPASE ACTIVITY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 %
Crystal growpH: 6.5
Details: 25% PEG MME 2000, 0.1M NA CACODYLATE, PH6.5, 0.2M MGCL2., pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 15, 2002 / Details: OSMIC BLUE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 20657 / % possible obs: 98.4 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 10.2
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.106 / Mean I/σ(I) obs: 3.4 / % possible all: 89.7

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YER
Resolution: 2→67.42 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.098 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE GLU A223 WAS THE LAST RESIDUE THAT WAS VISIBLE IN ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1036 5.1 %RANDOM
Rwork0.183 ---
Obs0.185 19286 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å20 Å2
2--0.61 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 2→67.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1634 0 24 274 1932
Refine LS restraints
Refinement-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221691
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.9762284
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.245207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0920.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021244
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.2804
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2208
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8261.51029
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5721664
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3033662
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0314.5618
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.322 55
Rwork0.256 1218

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