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- PDB-9d9h: Human Hsp90b nucleotide binding domain in complex with BRI2311 -

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Basic information

Entry
Database: PDB / ID: 9d9h
TitleHuman Hsp90b nucleotide binding domain in complex with BRI2311
ComponentsHeat shock protein HSP 90-beta
KeywordsCHAPERONE / HSP90 nucleotide binding domain inhibitor complex
Function / homology
Function and homology information


HSP90-CDC37 chaperone complex / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / histone methyltransferase binding / dynein axonemal particle / receptor ligand inhibitor activity / ATP-dependent protein binding / positive regulation of protein localization to cell surface / protein kinase regulator activity ...HSP90-CDC37 chaperone complex / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / histone methyltransferase binding / dynein axonemal particle / receptor ligand inhibitor activity / ATP-dependent protein binding / positive regulation of protein localization to cell surface / protein kinase regulator activity / protein folding chaperone complex / Respiratory syncytial virus genome replication / telomerase holoenzyme complex assembly / positive regulation of transforming growth factor beta receptor signaling pathway / Uptake and function of diphtheria toxin / dendritic growth cone / TPR domain binding / Assembly and release of respiratory syncytial virus (RSV) virions / The NLRP3 inflammasome / protein phosphatase activator activity / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / HSF1-dependent transactivation / response to unfolded protein / HSF1 activation / telomere maintenance via telomerase / Attenuation phase / chaperone-mediated protein complex assembly / axonal growth cone / RHOBTB2 GTPase cycle / Purinergic signaling in leishmaniasis infection / : / supramolecular fiber organization / DNA polymerase binding / heat shock protein binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / protein folding chaperone / peptide binding / cellular response to interleukin-4 / ESR-mediated signaling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / placenta development / nitric-oxide synthase regulator activity / positive regulation of cell differentiation / ATP-dependent protein folding chaperone / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Regulation of actin dynamics for phagocytic cup formation / kinase binding / tau protein binding / histone deacetylase binding / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / disordered domain specific binding / MHC class II protein complex binding / The role of GTSE1 in G2/M progression after G2 checkpoint / melanosome / unfolded protein binding / protein folding / double-stranded RNA binding / regulation of protein localization / cellular response to heat / secretory granule lumen / Estrogen-dependent gene expression / ficolin-1-rich granule lumen / Potential therapeutics for SARS / regulation of cell cycle / protein dimerization activity / protein stabilization / cadherin binding / neuronal cell body / ubiquitin protein ligase binding / Neutrophil degranulation / protein kinase binding / negative regulation of apoptotic process / virion attachment to host cell / perinuclear region of cytoplasm / SARS-CoV-2 activates/modulates innate and adaptive immune responses / cell surface / protein homodimerization activity / protein-containing complex / ATP hydrolysis activity / mitochondrion / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
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 superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
: / Heat shock protein HSP 90-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsKuntz, D.A. / Prive, G.G.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: To be published
Title: Final Title 'To Be Determined'
Authors: Kuntz, D.A. / Prive, G.G.
History
DepositionAug 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock protein HSP 90-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0217
Polymers25,1181
Non-polymers9036
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.348, 89.841, 97.315
Angle α, β, γ (deg.)90, 90, 90
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Heat shock protein HSP 90-beta / HSP 90 / Heat shock 84 kDa / HSP 84 / HSP84 / Heat shock protein family C member 3


Mass: 25118.373 Da / Num. of mol.: 1 / Fragment: nucleotide binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90AB1, HSP90B, HSPC2, HSPC3, HSPCB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08238
#2: Chemical ChemComp-A1A26 / (1P)-3-amino-6-[({1-[(2S)-2-(2,4-difluorophenyl)-2-hydroxy-3-(1H-1,2,4-triazol-1-yl)propyl]piperidin-4-yl}amino)methyl]-1-(4-phenyl-3,4-dihydro-2H-1,4-benzoxazin-6-yl)thieno[2,3-b]pyrazin-2(1H)-one


Mass: 725.810 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H37F2N9O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.93 Å3/Da / Density % sol: 58.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 21% PEG8000, 0.1M Hepes pH 7.5,1M LiCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.542 Å
DetectorType: DECTRIS EIGER R 1M / Detector: PIXEL / Date: May 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.96→24.51 Å / Num. obs: 21410 / % possible obs: 99.5 % / Redundancy: 5.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.038 / Rrim(I) all: 0.091 / Net I/σ(I): 12.3
Reflection shellResolution: 1.96→2.01 Å / % possible obs: 98.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.754 / Num. measured all: 4863 / Num. unique obs: 1476 / CC1/2: 0.671 / Rpim(I) all: 0.474 / Rrim(I) all: 0.897 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
CrysalisProdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→24.51 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20775 1066 -RANDOM
Rwork0.16259 ---
obs0.16479 20333 99.18 %-
Displacement parametersBiso mean: 29.682 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2---0.62 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.96→24.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1649 0 57 247 1953
LS refinement shellResolution: 1.96→2.03 Å /
Rfactor% reflection
Rfree0.278 -
Rwork0.245 -
obs-97.64 %
Refinement TLS params.Origin x: 0.2756 Å / Origin y: 14.9784 Å / Origin z: 20.7355 Å
111213212223313233
T0.0205 Å2-0.0005 Å20.0072 Å2-0.0108 Å2-0.0058 Å2--0.0077 Å2
L0.5952 °20.0963 °2-0.0373 °2-0.0804 °20.0119 °2--0.6436 °2
S-0.0005 Å °0.0289 Å °-0.0349 Å °0.0289 Å °-0.0012 Å °0.0203 Å °-0.0349 Å °0.0203 Å °0.0016 Å °

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