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- PDB-9d9g: Candida albicans Hsp90 nucleotide binding domain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9d9g
TitleCandida albicans Hsp90 nucleotide binding domain in complex with BRI2312
ComponentsHeat shock protein 90 homolog
KeywordsCHAPERONE / HSP90 nucleotide binding domain 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 / 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 90 homolog
Similarity search - Component
Biological speciesCandida albicans SC5314 (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsKuntz, D.A. / Prive, G.G.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Canada Foundation for Innovation 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

Downloads & links

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Assembly

Deposited unit
A: Heat shock protein 90 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6603
Polymers24,9101
Non-polymers7502
Water4,972276
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.054, 74.054, 107.513
Angle α, β, γ (deg.)90, 90, 90
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-469-

HOH

21A-582-

HOH

31A-601-

HOH

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Components

#1: Protein Heat shock protein 90 homolog


Mass: 24910.307 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans SC5314 (yeast)
Gene: HSP90, CAALFM_C702030WA, CaJ7.0234, CaO19.13868, CaO19.6515
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P46598
#2: Chemical ChemComp-A1A24 / (1P)-3-amino-6-[({1-[(2R)-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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.96 Å3/Da / Density % sol: 58.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 18% PEG6000, 0.1M Cacodylates pH 6.9, 0.2 M Mg Acetate, 20% glycerol

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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 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.68→26.893 Å / Num. obs: 34705 / % possible obs: 99.6 % / Redundancy: 11.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.015 / Rrim(I) all: 0.052 / Net I/σ(I): 30.6
Reflection shellResolution: 1.68→1.71 Å / % possible obs: 93.7 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.802 / Num. measured all: 4304 / Num. unique obs: 1625 / CC1/2: 0.567 / Rpim(I) all: 0.545 / Rrim(I) all: 0.979 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.82)refinement
Aimlessdata scaling
PHASERphasing
CrysalisProdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→26.893 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.731 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.079
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1829 1744 5.034 %
Rwork0.1624 32901 -
all0.163 --
obs-34645 99.492 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.714 Å2
Baniso -1Baniso -2Baniso -3
1-0.232 Å2-0 Å2-0 Å2
2--0.232 Å2-0 Å2
3----0.464 Å2
Refinement stepCycle: LAST / Resolution: 1.68→26.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1692 0 53 276 2021
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121865
X-RAY DIFFRACTIONr_bond_other_d0.0030.0161744
X-RAY DIFFRACTIONr_angle_refined_deg1.9731.8682536
X-RAY DIFFRACTIONr_angle_other_deg0.7941.7834027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7195232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.06358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.09810333
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.361087
X-RAY DIFFRACTIONr_chiral_restr0.0980.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022198
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02414
X-RAY DIFFRACTIONr_nbd_refined0.2110.2365
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1630.21589
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2933
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.2980
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2200
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1150.214
X-RAY DIFFRACTIONr_nbd_other0.130.293
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1440.241
X-RAY DIFFRACTIONr_mcbond_it2.5061.646907
X-RAY DIFFRACTIONr_mcbond_other2.5041.645907
X-RAY DIFFRACTIONr_mcangle_it4.052.9471146
X-RAY DIFFRACTIONr_mcangle_other4.0482.951147
X-RAY DIFFRACTIONr_scbond_it3.0441.871958
X-RAY DIFFRACTIONr_scbond_other3.0381.871958
X-RAY DIFFRACTIONr_scangle_it4.7663.3251390
X-RAY DIFFRACTIONr_scangle_other4.7643.3251391
X-RAY DIFFRACTIONr_lrange_it7.89518.662248
X-RAY DIFFRACTIONr_lrange_other7.70616.9162158
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.68-1.7230.2961290.28522640.28525310.9370.94394.54760.269
1.723-1.7710.2631210.24622910.24724240.9560.9699.50490.22
1.771-1.8220.1941220.20222790.20124010.9750.9751000.169
1.822-1.8770.2181120.17522070.17723190.9730.981000.142
1.877-1.9390.1891120.16821490.16922610.9780.9821000.137
1.939-2.0060.1821130.16520700.16621830.980.9831000.134
2.006-2.0820.1891060.15520010.15721070.9770.9851000.128
2.082-2.1660.1591020.1519390.1520410.9840.9871000.127
2.166-2.2620.193980.15218620.15419610.9740.98699.9490.128
2.262-2.3710.157910.14217840.14318750.9840.9881000.119
2.371-2.4980.179930.14917120.15118050.9820.9861000.126
2.498-2.6490.167840.15516130.15616970.9820.9861000.129
2.649-2.830.176820.15415310.15516150.9820.98699.87620.131
2.83-3.0530.161760.14114160.14214930.9810.98799.9330.123
3.053-3.3410.18680.14213310.14414000.9790.98799.92860.127
3.341-3.7280.16640.14212130.14312790.9860.98899.84360.133
3.728-4.2910.176580.13910730.14111330.9840.98899.82350.131
4.291-5.2220.154480.1449330.1459850.9830.98999.59390.14
5.222-7.2490.208390.2287470.2277860.9780.9731000.216
7.249-26.8930.225260.2164860.2175120.9440.9661000.204
Refinement TLS params.Method: refined / Origin x: -16.3281 Å / Origin y: -30.3712 Å / Origin z: -0.6719 Å
111213212223313233
T0.0102 Å20.0074 Å20.0066 Å2-0.0106 Å20.0155 Å2--0.0273 Å2
L0.4461 °2-0.0736 °20.0223 °2-0.4348 °2-0.007 °2--0.1234 °2
S0.0453 Å °0.0255 Å °0.0023 Å °-0.0176 Å °0.0083 Å °0.0193 Å °-0.004 Å °-0.0259 Å °-0.0536 Å °
Refinement TLS groupSelection: ALL

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