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- PDB-2iws: Radicicol analogues bound to the ATP site of HSP90 -

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Basic information

Entry
Database: PDB / ID: 2iws
TitleRadicicol analogues bound to the ATP site of HSP90
ComponentsATP-DEPENDENT MOLECULAR CHAPERONE HSP82
KeywordsCHAPERONE / INHIBITOR / HEAT SHOCK / ATP-BINDING / MULTIGENE FAMILY / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


The NLRP3 inflammasome / ESR-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / VEGFR2 mediated vascular permeability / HSF1-dependent transactivation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / response to oxygen levels ...The NLRP3 inflammasome / ESR-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / VEGFR2 mediated vascular permeability / HSF1-dependent transactivation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / response to oxygen levels / : / protein targeting to mitochondrion / box C/D snoRNP assembly / regulation of telomere maintenance / response to osmotic stress / 'de novo' protein folding / protein maturation / proteasome assembly / positive regulation of telomere maintenance via telomerase / Neutrophil degranulation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / cellular response to heat / protein refolding / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
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 ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and 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-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NP4 / ATP-dependent molecular chaperone HSP82
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRoe, S.M. / Prodromou, C. / Pearl, L.H.
CitationJournal: Chem.Biol. / Year: 2006
Title: Inhibition of Hsp90 with Synthetic Macrolactones: Synthesis and Structural and Biological Evaluation of Ring and Conformational Analogs of Radicicol.
Authors: Proisy, N. / Sharp, S.Y. / Boxall, K. / Connelly, S. / Roe, S.M. / Prodromou, C. / Slawin, A.M.Z. / Pearl, L.H. / Workman, P. / Moody, C.J.
History
DepositionJul 4, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
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: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5332
Polymers24,2091
Non-polymers3251
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)73.841, 73.841, 109.135
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-2009-

HOH

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Components

#1: Protein ATP-DEPENDENT MOLECULAR CHAPERONE HSP82 / HEAT SHOCK PROTEIN 90 HEAT-INDUCIBLE ISOFORM / 82 KDA HEAT SHOCK PROTEIN


Mass: 24208.582 Da / Num. of mol.: 1 / Fragment: N TERMINAL DOMAIN, RESIDUES 1-214
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02829
#2: Chemical ChemComp-NP4 / (5Z)-12-CHLORO-13,15-DIHYDROXY-4,7,8,9-TETRAHYDRO-2-BENZOXACYCLOTRIDECINE-1,10(3H,11H)-DIONE


Mass: 324.756 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17ClO5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMOLECULAR CHAPERONE THAT PROMOTES THE MATURATION, STRUCTURAL MAINTENANCE AND PROPER REGULATION OF ...MOLECULAR CHAPERONE THAT PROMOTES THE MATURATION, STRUCTURAL MAINTENANCE AND PROPER REGULATION OF SPECIFIC TARGET PROTEINS INVOLVED IN CELL CYCLE CONTROL AND SIGNAL TRANSDUCTION.

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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: 3.09 Å3/Da / Density % sol: 60 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 8730 / % possible obs: 99.6 % / Redundancy: 5 % / Biso Wilson estimate: 60 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.3
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.9 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AH6

1ah6


Resolution: 2.7→40 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.295 416 5 %RANDOM
Rwork0.223 ---
obs0.223 8716 99 %-
Solvent computationBsol: 71.2 Å2 / ksol: 0.383 e/Å3
Displacement parametersBiso mean: 48 Å2
Refinement stepCycle: LAST / Resolution: 2.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1673 0 22 77 1772
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.445
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d11.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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