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- PDB-9d9d: Candida albicans Hsp90 nucleotide binding domain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9d9d
TitleCandida albicans Hsp90 nucleotide binding domain in complex with BRI2216
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: 2.09 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: Candida albicans Hsp90 nucleotide binding domain complexes 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
B: Heat shock protein 90 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5603
Polymers49,8212
Non-polymers7401
Water3,531196
1
A: Heat shock protein 90 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6502
Polymers24,9101
Non-polymers7401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heat shock protein 90 homolog


Theoretical massNumber of molelcules
Total (without water)24,9101
Polymers24,9101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.041, 74.041, 108.811
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw

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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-A1A28 / (1P)-3-amino-N-{1-[(2R)-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 21% PEG6000, 0.1M Cacodylates pH 6.6, 0.2 M Ca 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: 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→28.3 Å / Num. obs: 37948 / % possible obs: 100 % / Redundancy: 8.5 % / Biso Wilson estimate: 25.16 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.045 / Rrim(I) all: 0.131 / Net I/σ(I): 15.2 / Num. measured all: 320744
Reflection shellResolution: 2.03→2.08 Å / % possible obs: 100 % / Redundancy: 5.9 % / Rmerge(I) obs: 1.04 / Num. measured all: 16461 / Num. unique obs: 2797 / CC1/2: 0.52 / Rpim(I) all: 0.469 / Rrim(I) all: 1.145 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
Aimlessdata scaling
CrysalisProdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→28.29 Å / SU ML: 0.2958 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.3761
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2667 1728 5 %
Rwork0.2183 32854 -
obs0.2207 34582 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.98 Å2
Refinement stepCycle: LAST / Resolution: 2.09→28.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3379 0 53 196 3628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00583609
X-RAY DIFFRACTIONf_angle_d1.03444895
X-RAY DIFFRACTIONf_chiral_restr0.0536552
X-RAY DIFFRACTIONf_plane_restr0.0073637
X-RAY DIFFRACTIONf_dihedral_angle_d17.04831343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.150.35481310.30332709X-RAY DIFFRACTION99.13
2.15-2.220.34741370.28172717X-RAY DIFFRACTION99.24
2.22-2.30.32291170.26162757X-RAY DIFFRACTION99.55
2.3-2.390.23551350.24862744X-RAY DIFFRACTION99.58
2.39-2.50.27361500.23992690X-RAY DIFFRACTION99.75
2.5-2.630.29231340.24662774X-RAY DIFFRACTION99.86
2.63-2.80.28911690.2362700X-RAY DIFFRACTION100
2.8-3.010.28411420.22182742X-RAY DIFFRACTION100
3.01-3.320.28351270.21042762X-RAY DIFFRACTION100
3.32-3.790.22611480.18572752X-RAY DIFFRACTION99.97
3.8-4.780.21931670.17072740X-RAY DIFFRACTION99.93
4.78-28.290.27631710.21962767X-RAY DIFFRACTION99.86
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)
11.482064472150.2961844251940.2903686978341.684426261340.4076682352971.31827923324-0.3153237333510.1099910568570.240862115277-0.3674119521930.1344665071810.829386771227-0.1966056535590.09392308747230.05223712137760.36449196301-0.117306513462-0.1153049895380.147376392981-0.009822469556820.4877269634176.59076962532-20.8889295151-0.895615248286
21.55799517379-0.9774232291470.01552246980880.7882622381110.6629911682842.532429215220.08199702438420.1726555481860.5452229221-0.502666888247-0.3525601330990.588973049401-0.583935419208-0.3926910119940.07295673141170.3693802166170.126627960702-0.05431545706170.23235208509-0.2095204111671.16153337777-3.75217487726-17.64679091812.08060775233
35.034212892640.03498728900920.9171285917998.51510606975-2.160638987677.056806398350.211050740979-0.225400261179-0.2421936372870.1843951169930.07680244430250.3674368667870.329434732105-0.427986967991-0.1576762863290.334746211194-0.0908875724073-0.0454532125190.1984960818640.05426523832820.4363835815438.13710316542-3.65066944997-7.14713212117
40.821358210160.5105784603270.227469373111.669390848340.3624209445611.60078789809-0.3803484278160.1995914647310.206765332861-0.5773313755030.1558510306110.561946128597-0.3419108352540.1294986627390.0202970790.354520615162-0.0805794799004-0.07738461671220.138802309588-0.03832739057950.479606666178.52347264803-26.0725393475-4.57784994686
56.28705543833-1.686088687550.4726196947193.60048777616-0.1961318397692.75577064959-0.0903047247082-0.736512614274-0.2195958261770.423268092149-0.0337831249530.5771277220480.2814253990430.06022521576350.08442029663120.265325101016-0.001396780225910.1016262573030.3974006052110.1275070132040.356079359423-0.341351749768-62.41849072338.07653736379
63.97071415406-0.2806408817122.501995690952.55462554525-0.8054984708792.114692849180.112720737470.180420973578-0.323510573251-0.2519601297540.03850770485760.009445929210810.4275205623020.228889888284-0.1024605428770.174179881430.0199659551709-0.01483950400150.129296285177-0.02629882293060.2055299790639.92770964269-56.9844041385-9.31246658279
72.72637933101-0.038712407113-0.0106233012551.77281687618-0.3535456858353.57207253135-0.0566216842899-0.09954634924770.236233936689-0.2542093426490.02065878863140.380506778046-0.150979751530.01366990225980.07344047463450.1671576401850.02495170759-0.041912784590.0676494450673-0.04481714535730.3132760264784.77591058363-47.977791471-6.90470587853
86.3902605874-3.081446739431.891250022413.86412024045-0.3882876590093.44569863295-0.0547087197382-0.0994287860492-0.840150768174-0.4446921018680.006905726228171.008503874480.591410695708-0.433265271163-0.1331894532960.412867215139-0.0301611869728-0.04821496296860.3323197750.06791870188890.5917671355621.96868281493-70.76099525012.37581612347
91.58084471229-1.264277473430.8070189346034.47955411597-1.771413178862.7865855831-0.0262617700901-0.233584832428-0.3323491431340.0208567870730.1031352129150.3212337708530.272778121731-0.0607616143029-0.06385224774420.1344096775880.00674982017939-0.01878531483360.1558214003190.02724851757320.2683389650186.58863129872-60.37835801123.43019062465
103.787717815960.300806811015-1.950219774612.354486688520.3778508214082.52813618718-0.0971616045224-0.06424068567-0.114982054230.127565030111-0.1929792539350.6673946755160.0474957754844-0.2716474072650.2488893293320.179432989329-0.00331561169787-0.006211471573460.171895896907-0.04909672074620.503759839862-4.40588161677-47.9213691948-2.34455242753
112.68319846570.2870497785060.2653351916741.56516692122-0.08178017489742.86995539986-0.166731718732-0.3878599130630.1255629539210.3292956148810.0601737933179-0.374713779041-0.08257223921140.4425863825790.09282449017680.1742751374480.0200500396464-0.06000510957270.263763076428-0.06195182625680.27937204218215.0899587764-50.49683984095.47735359332
120.2754606907060.6633151617790.05896042194335.04569804071.592954533183.03728624717-0.0774852103102-0.153588312480.2275490769280.3676804991660.327449563335-0.4677847513010.1327825835670.396227177793-0.206605756130.09070946393650.0287278283154-0.01651138962350.208737015959-0.1023956264660.30168053732219.7257050362-44.1413419753-3.63031334622
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 82 )AA4 - 821 - 79
22chain 'A' and (resid 83 through 98 )AA83 - 9880 - 95
33chain 'A' and (resid 99 through 123 )AA99 - 12396 - 120
44chain 'A' and (resid 124 through 218 )AA124 - 218121 - 215
55chain 'B' and (resid 4 through 29 )BD4 - 291 - 26
66chain 'B' and (resid 30 through 54 )BD30 - 5427 - 51
77chain 'B' and (resid 55 through 95 )BD55 - 9552 - 92
88chain 'B' and (resid 96 through 112 )BD96 - 11293 - 109
99chain 'B' and (resid 113 through 142 )BD113 - 142110 - 139
1010chain 'B' and (resid 143 through 172 )BD143 - 172140 - 169
1111chain 'B' and (resid 173 through 200 )BD173 - 200170 - 197
1212chain 'B' and (resid 201 through 218 )BD201 - 218198 - 215

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