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- PDB-1uyi: Human Hsp90-alpha with 8-(2,5-dimethoxy-benzyl)-2-fluoro-9-pent-9... -

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Basic information

Entry
Database: PDB / ID: 1uyi
TitleHuman Hsp90-alpha with 8-(2,5-dimethoxy-benzyl)-2-fluoro-9-pent-9H-purin-6-ylamine
ComponentsHEAT SHOCK PROTEIN HSP 90-ALPHA
KeywordsCHAPERONE / HSP90 / ATPASE / PUZ / ATP-BINDING / HEAT SHOCK
Function / homology
Function and homology information


sulfonylurea receptor binding / sperm mitochondrial sheath / dATP binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / Scavenging by Class F Receptors / UTP binding / sperm plasma membrane / chaperone-mediated autophagy ...sulfonylurea receptor binding / sperm mitochondrial sheath / dATP binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / Scavenging by Class F Receptors / UTP binding / sperm plasma membrane / chaperone-mediated autophagy / Rho GDP-dissociation inhibitor binding / Respiratory syncytial virus genome replication / telomerase holoenzyme complex assembly / mitochondrial transport / Uptake and function of diphtheria toxin / 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 / protein insertion into mitochondrial outer membrane / TPR domain binding / dendritic growth cone / Assembly and release of respiratory syncytial virus (RSV) virions / PIWI-interacting RNA (piRNA) biogenesis / non-chaperonin molecular chaperone ATPase / Sema3A PAK dependent Axon repulsion / protein unfolding / regulation of protein ubiquitination / positive regulation of cell size / HSF1-dependent transactivation / response to unfolded protein / enzyme-substrate adaptor activity / HSF1 activation / skeletal muscle contraction / regulation of protein-containing complex assembly / axonal growth cone / telomere maintenance via telomerase / Attenuation phase / chaperone-mediated protein complex assembly / regulation of postsynaptic membrane neurotransmitter receptor levels / neurofibrillary tangle assembly / RHOBTB2 GTPase cycle / positive regulation of lamellipodium assembly / eNOS activation / nitric oxide metabolic process / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / DNA polymerase binding / positive regulation of defense response to virus by host / response to salt stress / Signaling by ERBB2 / positive regulation of telomere maintenance via telomerase / cardiac muscle cell apoptotic process / positive regulation of cardiac muscle contraction / endocytic vesicle lumen / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / activation of innate immune response / Recruitment of NuMA to mitotic centrosomes / lysosomal lumen / Anchoring of the basal body to the plasma membrane / nitric-oxide synthase regulator activity / positive regulation of interferon-beta production / ESR-mediated signaling / protein tyrosine kinase binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to cold / Constitutive Signaling by Overexpressed ERBB2 / AURKA Activation by TPX2 / VEGFR2 mediated vascular permeability / response to cocaine / brush border membrane / ATP-dependent protein folding chaperone / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Signaling by ERBB2 KD Mutants / Regulation of actin dynamics for phagocytic cup formation / cellular response to virus / Regulation of necroptotic cell death / tau protein binding / positive regulation of protein import into nucleus / VEGFA-VEGFR2 Pathway / response to estrogen / Downregulation of ERBB2 signaling / histone deacetylase binding / neuron migration / Chaperone Mediated Autophagy / positive regulation of protein catabolic process / Aggrephagy / positive regulation of nitric oxide biosynthetic process / MHC class II protein complex binding / disordered domain specific binding
Similarity search - Function
Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase ...Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PUZ / Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWright, L. / Barril, X. / Dymock, B. / Sheridan, L. / Surgenor, A. / Beswick, M. / Drysdale, M. / Collier, A. / Massey, A. / Davies, N. ...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.
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.
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
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)26,9802
Polymers26,6111
Non-polymers3691
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)66.956, 90.874, 99.576
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 26610.807 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-PUZ / 8-(2,5-DIMETHOXY-BENZYL)-2-FLUORO-9-PENT-9H-PURIN-6-YLAMINE


Mass: 369.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20FN5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE CONFLICT THR62SER IS DOCUMENTED IN REFERENCES THAT ACCOMPANY THE CORRESPONDING UNIPROT ENTRY

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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: 2.2→30 Å / Num. obs: 15126 / % possible obs: 95.9 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 12
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 3 / % possible all: 89.9

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Processing

Software
NameClassification
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YER

1yer


Resolution: 2.2→67.42 Å / SU B: 3.098 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.141
Details: RESIDUE GLU A223 WAS THE LAST RESIDUE THAT WAS VISIBLE IN ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.21814 1036 5.1 %RANDOM
Rwork0.18334 ---
obs-19286 94.2 %-
Displacement parametersBiso mean: 28.336 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å20 Å2
2--0.61 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.2→67.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1635 0 27 263 1925

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