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- PDB-9d9e: Candida albicans Hsp90 nucleotide binding domain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9d9e
TitleCandida albicans Hsp90 nucleotide binding domain in complex with BRI2217
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: 2.03 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 17, 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
B: Heat shock protein 90 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7526
Polymers49,8212
Non-polymers9324
Water5,278293
1
A: Heat shock protein 90 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7283
Polymers24,9101
Non-polymers8182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heat shock protein 90 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0243
Polymers24,9101
Non-polymers1142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.806, 80.448, 121.756
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Heat shock protein 90 homolog


Mass: 24910.307 Da / Num. of mol.: 2
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-A1A27 / (1P)-3-amino-N-{1-[(2S)-2-(2,4-difluorophenyl)-2-hydroxy-3-(1H-1,2,4-triazol-1-yl)propyl]piperidin-4-yl}-2-oxo-1-(4-phenyl-3,4-dihydro-2H-1,4-benzoxazin-6-yl)-1,2-dihydrothieno[2,3-b]pyrazine-6-carboxamide


Mass: 739.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H35F2N9O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.3 Å3/Da / Density % sol: 46.54 % / Description: Flat morphology
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 24% PEG6000, 0.1M Cacodylates pH 6.2, 0.2 M Ca Acetate, 20% glycerol. Grew on fiber contaminant

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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: Jun 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.03→29.59 Å / Num. obs: 30512 / % possible obs: 99.9 % / Redundancy: 5.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.051 / Rrim(I) all: 0.121 / Net I/σ(I): 11.9 / Num. measured all: 168266
Reflection shellResolution: 2.03→2.08 Å / % possible obs: 100 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.703 / Num. measured all: 9387 / Num. unique obs: 2201 / CC1/2: 0.777 / Rpim(I) all: 0.381 / Rrim(I) all: 0.803 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
Aimlessdata scaling
CrysalisProdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→29.59 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2275 1456 4.78 %
Rwork0.1807 --
obs0.1829 30439 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.03→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3338 0 62 293 3693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123550
X-RAY DIFFRACTIONf_angle_d1.264813
X-RAY DIFFRACTIONf_dihedral_angle_d16.2261313
X-RAY DIFFRACTIONf_chiral_restr0.067543
X-RAY DIFFRACTIONf_plane_restr0.01626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.10.31931500.23812845X-RAY DIFFRACTION100
2.1-2.190.29831400.21582821X-RAY DIFFRACTION100
2.19-2.290.26791380.19062879X-RAY DIFFRACTION100
2.29-2.410.24681660.19192826X-RAY DIFFRACTION100
2.41-2.560.2321400.18932884X-RAY DIFFRACTION100
2.56-2.750.26751410.18872917X-RAY DIFFRACTION100
2.75-3.030.2261220.17312872X-RAY DIFFRACTION100
3.03-3.470.20981620.17352915X-RAY DIFFRACTION100
3.47-4.370.19241430.14682952X-RAY DIFFRACTION100
4.37-29.590.20311540.18783072X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5303-0.3744-0.68833.08021.78353.50280.04840.1253-0.0656-0.3773-0.0438-0.0626-0.17960.0856-0.01910.12450.0235-0.01580.170.04950.12153.740912.39985.594
24.1965-1.3902-0.3263.82490.82912.6533-0.1574-0.0688-0.10310.0490.0950.0939-0.0137-0.05080.06450.078-0.01740.03050.10980.04390.1040.499712.364617.3276
35.7394-2.5336-3.98058.24960.1199.7568-0.26510.2754-0.2382-0.0420.040.28550.00530.03820.13180.1660.02410.00830.29670.06260.22687.469916.8829-5.5543
42.99380.2632-0.42291.6805-0.20712.9297-0.03460.1034-0.2936-0.1008-0.0506-0.10570.24060.1680.06590.1210.0243-0.00280.1280.00940.14025.30946.582713.1547
53.64370.41510.58153.8518-2.05547.6590.01220.06690.6427-0.1927-0.3915-1.45190.2680.6750.34710.1397-0.0587-0.01170.21770.0440.343613.769216.182821.5762
61.26530.00360.30472.07410.50043.0197-0.0343-0.23380.16040.43020.0354-0.0794-0.43720.025-0.00010.38420.0246-0.05340.1635-0.00490.189510.0759.754750.0363
74.78862.60460.15134.2141-0.56222.99-0.0024-0.10850.14680.26460.08630.149-0.3098-0.228-0.09370.19730.0653-0.02720.12810.020.14293.46288.681739.1313
83.5181-0.46322.31982.0238-1.04483.5616-0.1803-0.2290.15610.47020.0525-0.2143-0.76720.00740.11450.40310.0158-0.00590.176-0.04150.215912.900511.06354.2785
93.261-1.647-0.79845.03152.62516.7439-0.087-0.24170.27850.38180.18080.1237-0.7839-0.52850.00660.35130.13160.03660.28340.01840.2228-3.262514.908942.906
103.60830.7722-0.54121.7090.58693.8716-0.0560.11860.2550.23750.055-0.1605-0.5060.4948-0.01510.2668-0.051-0.06280.18350.04390.210917.174914.370936.4422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 54 )
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 100 )
3X-RAY DIFFRACTION3chain 'A' and (resid 101 through 125 )
4X-RAY DIFFRACTION4chain 'A' and (resid 126 through 200 )
5X-RAY DIFFRACTION5chain 'A' and (resid 201 through 216 )
6X-RAY DIFFRACTION6chain 'B' and (resid 6 through 54 )
7X-RAY DIFFRACTION7chain 'B' and (resid 55 through 100 )
8X-RAY DIFFRACTION8chain 'B' and (resid 101 through 142 )
9X-RAY DIFFRACTION9chain 'B' and (resid 143 through 172 )
10X-RAY DIFFRACTION10chain 'B' and (resid 173 through 217 )

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