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- PDB-9msx: Candida albicans Hsp90 nucleotide binding domain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9msx
TitleCandida albicans Hsp90 nucleotide binding domain in complex with TAS116
ComponentsHeat shock protein 90 homolog
KeywordsCHAPERONE/INHIBITOR / Inhibitor complex / CHAPERONE / CHAPERONE-INHIBITOR complex
Function / homology
Function and homology information


negative regulation of filamentous growth of a population of unicellular organisms / filamentous growth of a population of unicellular organisms / hyphal cell wall / fungal-type cell wall / filamentous growth / nuclear receptor-mediated steroid hormone signaling pathway / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / extracellular vesicle ...negative regulation of filamentous growth of a population of unicellular organisms / filamentous growth of a population of unicellular organisms / hyphal cell wall / fungal-type cell wall / filamentous growth / nuclear receptor-mediated steroid hormone signaling pathway / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / extracellular vesicle / cellular response to heat / regulation of apoptotic process / protein stabilization / perinuclear region of cytoplasm / cell surface / protein-containing complex / ATP hydrolysis activity / mitochondrion / ATP binding / membrane / 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 ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
: / Heat shock protein 90 homolog
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKowalewski, M.E. / Redinbo, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM148376-01A1 United States
CitationJournal: Biochemistry / Year: 2025
Title: Structural Insights into Selectively Targeting Candida albicans Hsp90.
Authors: Kowalewski, M.E. / Zagler, S. / Redinbo, M.R.
History
DepositionJan 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heat shock protein 90 homolog
B: Heat shock protein 90 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7356
Polymers52,7022
Non-polymers1,0334
Water1,65792
1
A: Heat shock protein 90 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8052
Polymers26,3511
Non-polymers4551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heat shock protein 90 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9304
Polymers26,3511
Non-polymers5793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.907, 47.907, 342.687
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein Heat shock protein 90 homolog


Mass: 26350.838 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast)
Gene: HSP90, CAALFM_C702030WA, CaJ7.0234, CaO19.13868, CaO19.6515
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P46598
#2: Chemical ChemComp-A1BPC / (4P)-3-ethyl-4-[(4P)-4-[(4M)-4-(1-methyl-1H-pyrazol-4-yl)-1H-imidazol-1-yl]-3-(propan-2-yl)-1H-pyrazolo[3,4-b]pyridin-1-yl]benzamide / Tas-116 / Pimitespib / Jeselhy


Mass: 454.527 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H26N8O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Bis-Tris (pH6.5) and 20% w/v PEG5000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→57.11 Å / Num. obs: 15296 / % possible obs: 99.72 % / Redundancy: 11.6 % / Biso Wilson estimate: 38.12 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.193 / Net I/σ(I): 9.18
Reflection shellResolution: 2.5→2.58 Å / Redundancy: 10.9 % / Rmerge(I) obs: 1.387 / Mean I/σ(I) obs: 2.33 / Num. unique obs: 1397 / CC1/2: 0.885 / % possible all: 99.43

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
PHASERphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→57.11 Å / SU ML: 0.3705 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 29.1831
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2574 1533 10.05 %
Rwork0.1766 13719 -
obs0.1847 15252 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.99 Å2
Refinement stepCycle: LAST / Resolution: 2.5→57.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3354 0 76 92 3522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01193494
X-RAY DIFFRACTIONf_angle_d1.2744727
X-RAY DIFFRACTIONf_chiral_restr0.0582537
X-RAY DIFFRACTIONf_plane_restr0.0129606
X-RAY DIFFRACTIONf_dihedral_angle_d17.5331280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.580.34921420.22891246X-RAY DIFFRACTION99.57
2.58-2.670.31441370.21981254X-RAY DIFFRACTION99.5
2.67-2.780.35271350.23171231X-RAY DIFFRACTION99.35
2.78-2.910.25831370.21281225X-RAY DIFFRACTION99.85
2.91-3.060.32341400.19561254X-RAY DIFFRACTION99.79
3.06-3.250.26861410.20541257X-RAY DIFFRACTION99.64
3.25-3.50.31241390.19141242X-RAY DIFFRACTION99.93
3.5-3.850.2771430.15881234X-RAY DIFFRACTION99.78
3.86-4.410.23531430.13961269X-RAY DIFFRACTION100
4.41-5.560.1841410.14361242X-RAY DIFFRACTION99.78
5.56-57.110.21911350.17731265X-RAY DIFFRACTION99.86

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