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- PDB-5ucj: Hsp90b N-terminal domain with inhibitors -

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Basic information

Entry
Database: PDB / ID: 5ucj
TitleHsp90b N-terminal domain with inhibitors
ComponentsHeat shock protein HSP 90-betaHeat shock response
KeywordsChaperone/Inhibitor / Hsp90 inhibitor / Chaperone-Inhibitor complex
Function / homology
Function and homology information


: / HSP90-CDC37 chaperone complex / positive regulation of cyclin-dependent protein kinase activity / Aryl hydrocarbon receptor signalling / negative regulation of proteasomal protein catabolic process / dynein axonemal particle / aryl hydrocarbon receptor complex / histone methyltransferase binding / protein kinase regulator activity / positive regulation of protein localization to cell surface ...: / HSP90-CDC37 chaperone complex / positive regulation of cyclin-dependent protein kinase activity / Aryl hydrocarbon receptor signalling / negative regulation of proteasomal protein catabolic process / dynein axonemal particle / aryl hydrocarbon receptor complex / histone methyltransferase binding / protein kinase regulator activity / positive regulation of protein localization to cell surface / ATP-dependent protein binding / negative regulation of protein metabolic process / positive regulation of tau-protein kinase activity / telomerase holoenzyme complex assembly / Uptake and function of diphtheria toxin / TPR domain binding / positive regulation of transforming growth factor beta receptor signaling pathway / dendritic growth cone / positive regulation of phosphoprotein phosphatase activity / Sema3A PAK dependent Axon repulsion / The NLRP3 inflammasome / regulation of protein ubiquitination / HSF1-dependent transactivation / telomere maintenance via telomerase / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / response to unfolded protein / HSF1 activation / chaperone-mediated protein complex assembly / Attenuation phase / RHOBTB2 GTPase cycle / DNA polymerase binding / Purinergic signaling in leishmaniasis infection / supramolecular fiber organization / axonal growth cone / positive regulation of telomerase activity / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / cellular response to interleukin-4 / nitric-oxide synthase regulator activity / ESR-mediated signaling / placenta development / positive regulation of cell differentiation / peptide binding / ATP-dependent protein folding chaperone / tau protein binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Regulation of actin dynamics for phagocytic cup formation / kinase binding / Chaperone Mediated Autophagy / histone deacetylase binding / The role of GTSE1 in G2/M progression after G2 checkpoint / positive regulation of nitric oxide biosynthetic process / regulation of protein localization / disordered domain specific binding / melanosome / unfolded protein binding / double-stranded RNA binding / protein folding / cellular response to heat / MHC class II protein complex binding / secretory granule lumen / Estrogen-dependent gene expression / ficolin-1-rich granule lumen / Potential therapeutics for SARS / protein stabilization / protein dimerization activity / regulation of cell cycle / cadherin binding / neuronal cell body / ubiquitin protein ligase binding / Neutrophil degranulation / virion attachment to host cell / negative regulation of apoptotic process / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / cell surface / ATP hydrolysis activity / protein homodimerization activity / protein-containing complex / mitochondrion / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane / 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-KU3 / Heat shock protein HSP 90-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.693 Å
AuthorsPeng, S. / Balch, M. / Matts, R. / Deng, J.
CitationJournal: Nat Commun / Year: 2018
Title: Structure-guided design of an Hsp90 beta N-terminal isoform-selective inhibitor.
Authors: Khandelwal, A. / Kent, C.N. / Balch, M. / Peng, S. / Mishra, S.J. / Deng, J. / Day, V.W. / Liu, W. / Subramanian, C. / Cohen, M. / Holzbeierlein, J.M. / Matts, R. / Blagg, B.S.J.
History
DepositionDec 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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-beta
B: Heat shock protein HSP 90-beta
C: Heat shock protein HSP 90-beta
D: Heat shock protein HSP 90-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,16114
Polymers98,3314
Non-polymers1,83010
Water11,908661
1
A: Heat shock protein HSP 90-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0794
Polymers24,5831
Non-polymers4973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heat shock protein HSP 90-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0794
Polymers24,5831
Non-polymers4973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Heat shock protein HSP 90-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0013
Polymers24,5831
Non-polymers4182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Heat shock protein HSP 90-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0013
Polymers24,5831
Non-polymers4182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.464, 129.464, 106.357
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
Heat shock protein HSP 90-beta / Heat shock response / HSP 90 / Heat shock 84 kDa / HSP84


Mass: 24582.738 Da / Num. of mol.: 4 / Fragment: UNP residues 1-218
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90AB1, HSP90B, HSPC2, HSPCB / Production host: Escherichia coli (E. coli) / References: UniProt: P08238
#2: Chemical
ChemComp-KU3 / (5-fluoroisoindolin-2-yl)(4-hydroxy-5-isopropylbenzo[d]isoxazol-7-yl)methanone / (5-fluoro-1,3-dihydro-2H-isoindol-2-yl)[4-hydroxy-7-(propan-2-yl)-1,2-benzoxazol-5-yl]methanone


Mass: 340.348 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H17FN2O3
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 661 / Source method: isolated from a natural source / Formula: H2O

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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: 2.62 Å3/Da / Density % sol: 52.99 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 30% PEG 8,000, 0.2 M sodium acetate, 0.1 sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 112035 / % possible obs: 100 % / Redundancy: 5.7 % / Rsym value: 0.091 / Net I/σ(I): 23
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.677 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UYM

1uym


Resolution: 1.693→42.377 Å / SU ML: 0.19 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 20.4
RfactorNum. reflection% reflection
Rfree0.1966 5666 5.06 %
Rwork0.1737 --
obs0.1749 111987 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.693→42.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6702 0 124 661 7487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086952
X-RAY DIFFRACTIONf_angle_d1.0049396
X-RAY DIFFRACTIONf_dihedral_angle_d24.1252554
X-RAY DIFFRACTIONf_chiral_restr0.1721054
X-RAY DIFFRACTIONf_plane_restr0.0051196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.693-1.71220.29231670.24953215X-RAY DIFFRACTION91
1.7122-1.73240.29331910.24383523X-RAY DIFFRACTION100
1.7324-1.75350.25691700.23353555X-RAY DIFFRACTION100
1.7535-1.77570.26832460.22493532X-RAY DIFFRACTION100
1.7757-1.79910.2451640.22253568X-RAY DIFFRACTION100
1.7991-1.82370.27691910.22073516X-RAY DIFFRACTION100
1.8237-1.84980.23872200.20953532X-RAY DIFFRACTION100
1.8498-1.87740.25071700.21433559X-RAY DIFFRACTION100
1.8774-1.90670.24811770.20543543X-RAY DIFFRACTION100
1.9067-1.9380.26771860.21083567X-RAY DIFFRACTION100
1.938-1.97140.25961890.21193537X-RAY DIFFRACTION100
1.9714-2.00720.22322200.19833484X-RAY DIFFRACTION100
2.0072-2.04580.22111920.19493579X-RAY DIFFRACTION100
2.0458-2.08760.25761800.1953571X-RAY DIFFRACTION100
2.0876-2.1330.23292050.19493497X-RAY DIFFRACTION100
2.133-2.18260.22012040.19113539X-RAY DIFFRACTION100
2.1826-2.23720.21961780.18273588X-RAY DIFFRACTION100
2.2372-2.29770.18261790.18373530X-RAY DIFFRACTION100
2.2977-2.36530.2061960.18553556X-RAY DIFFRACTION100
2.3653-2.44160.22011650.18383593X-RAY DIFFRACTION100
2.4416-2.52890.22362020.18753516X-RAY DIFFRACTION100
2.5289-2.63010.19791800.18063564X-RAY DIFFRACTION100
2.6301-2.74980.21372020.18413557X-RAY DIFFRACTION100
2.7498-2.89470.20321750.17753584X-RAY DIFFRACTION100
2.8947-3.07610.21511740.18353563X-RAY DIFFRACTION100
3.0761-3.31350.19622010.18613562X-RAY DIFFRACTION100
3.3135-3.64680.19961650.16523596X-RAY DIFFRACTION100
3.6468-4.1740.171930.15093577X-RAY DIFFRACTION100
4.174-5.25730.1361820.13543580X-RAY DIFFRACTION100
5.2573-42.39030.18022020.16333638X-RAY DIFFRACTION100

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