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- PDB-7d1v: Hsp90 alpha N-terminal domain in complex with a 6C compund -

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Basic information

Entry
Database: PDB / ID: 7d1v
TitleHsp90 alpha N-terminal domain in complex with a 6C compund
ComponentsHeat shock protein HSP 90-alphaHeat shock response
KeywordsCHAPERONE/INHIBITOR / CHAPERONE-Inhibitor complex
Function / homology
Function and homology information


Drug-mediated inhibition of ERBB2 signaling / ESR-mediated signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / HSF1-dependent transactivation / Signaling by ERBB2 / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / HSF1 activation / RHOBTB2 GTPase cycle / Sema3A PAK dependent Axon repulsion ...Drug-mediated inhibition of ERBB2 signaling / ESR-mediated signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / HSF1-dependent transactivation / Signaling by ERBB2 / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / HSF1 activation / RHOBTB2 GTPase cycle / Sema3A PAK dependent Axon repulsion / Downregulation of ERBB2 signaling / Attenuation phase / Regulation of necroptotic cell death / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / VEGFR2 mediated vascular permeability / positive regulation of cytotoxic T cell differentiation / Extra-nuclear estrogen signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Regulation of actin dynamics for phagocytic cup formation / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition / Estrogen-dependent gene expression / VEGFA-VEGFR2 Pathway / sperm mitochondrial sheath / dATP binding / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / UTP binding / sperm plasma membrane / protein insertion into mitochondrial outer membrane / telomerase holoenzyme complex assembly / Rho GDP-dissociation inhibitor binding / TPR domain binding / non-chaperonin molecular chaperone ATPase / regulation of postsynaptic membrane neurotransmitter receptor levels / dendritic growth cone / skeletal muscle contraction / regulation of protein ubiquitination / positive regulation of cell size / telomere maintenance via telomerase / response to unfolded protein / chaperone-mediated protein complex assembly / sperm flagellum / positive regulation of lamellipodium assembly / DNA polymerase binding / axonal growth cone / protein folding chaperone / positive regulation of cardiac muscle contraction / cardiac muscle cell apoptotic process / response to salt stress / positive regulation of defense response to virus by host / protein tyrosine kinase binding / nitric oxide biosynthetic process / Neutrophil degranulation / response to cold / activation of innate immune response / positive regulation of interferon-beta production / nitric-oxide synthase regulator activity / response to cocaine / brush border membrane / ATP-dependent protein folding chaperone / neuron migration / tau protein binding / cellular response to virus / positive regulation of protein import into nucleus / response to estrogen / histone deacetylase binding / positive regulation of protein catabolic process / regulation of protein localization / positive regulation of nitric oxide biosynthetic process / disordered domain specific binding / unfolded protein binding / melanosome / protein folding / GTPase binding / myelin sheath / cellular response to heat / response to heat / protein refolding / scaffold protein binding / basolateral plasma membrane / protein phosphatase binding / collagen-containing extracellular matrix / regulation of apoptotic process / transmembrane transporter binding / protein stabilization / response to xenobiotic stimulus / positive regulation of protein phosphorylation / apical plasma membrane / response to antibiotic / mRNA binding / neuronal cell body / ubiquitin protein ligase binding / GTP 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-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Chem-GOU / Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.332 Å
AuthorsShin, S.C. / Kim, E.E.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2020R1A6A3A01095791 Korea, Republic Of
CitationJournal: Int J Mol Sci / Year: 2020
Title: Structural Basis for Design of New Purine-Based Inhibitors Targeting the Hydrophobic Binding Pocket of Hsp90.
Authors: Shin, S.C. / El-Damasy, A.K. / Lee, J.H. / Seo, S.H. / Kim, J.H. / Seo, Y.H. / Lee, Y. / Yu, J.H. / Bang, E.K. / Kim, E.E. / Keum, G.
History
DepositionSep 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)24,6953
Polymers24,1091
Non-polymers5852
Water7,548419
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10420 Å2
Unit cell
Length a, b, c (Å)67.105, 90.088, 98.714
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Heat shock protein HSP 90-alpha / Heat shock response / Heat shock 86 kDa / HSP86 / Tumor-specific transplantation 86 kDa antigen / TSTA


Mass: 24109.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hsp90aa1, Hsp86, Hsp86-1, Hspca / Production host: Escherichia coli (E. coli) / References: UniProt: P07901
#2: Chemical ChemComp-GOU / 6-chloranyl-9-[(3-propan-2-yl-1,2-oxazol-5-yl)methyl]purin-2-amine


Mass: 292.724 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H13ClN6O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.19 Å3/Da / Density % sol: 61.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 1.0M ammonium Sulfate, 0.1M Tris-HCl (pH8.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.33→50 Å / Num. obs: 68098 / % possible obs: 99.3 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.056 / Χ2: 1.6 / Net I/σ(I): 15.9 / Num. measured all: 734331
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.33-1.3870.32866460.869198
1.38-1.438.10.29367300.938199.1
1.43-1.58.80.23967541.045199.4
1.5-1.589.60.18567481.192199.6
1.58-1.6810.30.14668131.285199.6
1.68-1.8111.10.10768121.433199.8
1.81-1.9912.10.07868031.693199.8
1.99-2.2713.20.0668851.984199.9
2.27-2.8713.70.04969222.057199.9
2.87-5013.80.04169852.332198

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H22

5h22


Resolution: 1.332→29.959 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 17.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1938 2000 2.94 %
Rwork0.1788 66098 -
obs0.1792 68098 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 50.03 Å2 / Biso mean: 17.972 Å2 / Biso min: 7.65 Å2
Refinement stepCycle: final / Resolution: 1.332→29.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1642 0 40 419 2101
Biso mean--12.62 28.69 -
Num. residues----209
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.332-1.3650.2449139460798
1.365-1.40190.25261410.2333464699
1.4019-1.44310.24151410.2217466099
1.4431-1.48970.22691420.2034469099
1.4897-1.54290.18751410.18424671100
1.5429-1.60470.18791430.17284698100
1.6047-1.67770.19481430.17084730100
1.6777-1.76620.18931420.17164713100
1.7662-1.87680.19161440.16684737100
1.8768-2.02170.18871430.16624742100
2.0217-2.22510.17031430.16224735100
2.2251-2.54690.18361440.1764780100
2.5469-3.20830.21581480.18394838100

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