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- PDB-7k9u: Cryptococcus neoformans Hsp90 nucleotide binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 7k9u
TitleCryptococcus neoformans Hsp90 nucleotide binding domain in complex with BUCMD00429
ComponentsHsp90-like protein
KeywordsCHAPERONE / Cryptococcus / HSP90 / ATP-binding / Inhibitor
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Histidine kinase/HSP90-like ATPase / 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-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases ...Histidine kinase/HSP90-like ATPase / 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-, 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
Chem-W8Y / Hsp90-like protein
Similarity search - Component
Biological speciesCryptococcus neoformans (Cryptococcus neoformans serotype A)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsKuntz, D.A. / Prive, G.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01AI120958 United States
CitationJournal: J.Med.Chem. / Year: 2021
Title: Fungal-Selective Resorcylate Aminopyrazole Hsp90 Inhibitors: Optimization of Whole-Cell Anticryptococcal Activity and Insights into the Structural Origins of Cryptococcal Selectivity.
Authors: Marcyk, P.T. / LeBlanc, E.V. / Kuntz, D.A. / Xue, A. / Ortiz, F. / Trilles, R. / Bengtson, S. / Kenney, T.M.G. / Huang, D.S. / Robbins, N. / Williams, N.S. / Krysan, D.J. / Prive, G.G. / ...Authors: Marcyk, P.T. / LeBlanc, E.V. / Kuntz, D.A. / Xue, A. / Ortiz, F. / Trilles, R. / Bengtson, S. / Kenney, T.M.G. / Huang, D.S. / Robbins, N. / Williams, N.S. / Krysan, D.J. / Prive, G.G. / Whitesell, L. / Cowen, L.E. / Brown, L.E.
History
DepositionSep 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: 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
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hsp90-like protein
B: Hsp90-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8024
Polymers48,9472
Non-polymers8552
Water3,531196
1
A: Hsp90-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9012
Polymers24,4741
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hsp90-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9012
Polymers24,4741
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.117, 44.328, 77.444
Angle α, β, γ (deg.)90.000, 103.804, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Hsp90-like protein


Mass: 24473.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans (Cryptococcus neoformans serotype A)
Production host: Escherichia coli (E. coli) / References: UniProt: J9VVA4
#2: Chemical ChemComp-W8Y / (5,7-dihydro-6H-pyrrolo[3,4-b]pyridin-6-yl){2,4-dihydroxy-6-[(1-methyl-3-phenyl-1H-pyrazol-5-yl)amino]phenyl}methanone


Mass: 427.455 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H21N5O3 / 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

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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: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1M LiCl, HEPES pH 7, 20-25% PEG 6K, 10-20% DMSO

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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: 0.978 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.92→29.46 Å / Num. obs: 36323 / % possible obs: 99.2 % / Redundancy: 6.7 % / Biso Wilson estimate: 40.53 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.027 / Rrim(I) all: 0.068 / Net I/σ(I): 16.7
Reflection shellResolution: 1.92→1.96 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.881 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3444 / CC1/2: 0.867 / Rpim(I) all: 0.372 / Rrim(I) all: 0.959 / % possible all: 89.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CJI

6cji


Resolution: 1.92→29.45 Å / SU ML: 0.251 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.6421
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2341 2627 3.74 %
Rwork0.2112 67541 -
obs0.2121 70168 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.63 Å2
Refinement stepCycle: LAST / Resolution: 1.92→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 0 64 196 3438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01073305
X-RAY DIFFRACTIONf_angle_d1.19964473
X-RAY DIFFRACTIONf_chiral_restr0.0863512
X-RAY DIFFRACTIONf_plane_restr0.0073567
X-RAY DIFFRACTIONf_dihedral_angle_d20.29671206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.960.45241200.36913137X-RAY DIFFRACTION87.7
1.96-20.35881590.34153592X-RAY DIFFRACTION98.87
2-2.040.33541390.32743580X-RAY DIFFRACTION98.99
2.04-2.080.32541300.31513518X-RAY DIFFRACTION98.94
2.08-2.130.30041330.30023580X-RAY DIFFRACTION99.3
2.13-2.180.29221270.27533608X-RAY DIFFRACTION99.02
2.18-2.240.3081390.27693524X-RAY DIFFRACTION99.08
2.24-2.310.26741180.26433610X-RAY DIFFRACTION98.91
2.31-2.380.31131290.26483532X-RAY DIFFRACTION99.16
2.38-2.470.27431420.25373636X-RAY DIFFRACTION99.24
2.47-2.570.28671260.25453544X-RAY DIFFRACTION99.27
2.57-2.680.31051340.2543588X-RAY DIFFRACTION99.52
2.68-2.830.24781570.22573568X-RAY DIFFRACTION99.73
2.83-30.26071530.21983616X-RAY DIFFRACTION99.84
3-3.230.23921660.20733546X-RAY DIFFRACTION99.81
3.23-3.560.2121180.19323618X-RAY DIFFRACTION99.84
3.56-4.070.19491350.17493620X-RAY DIFFRACTION99.81
4.07-5.130.17441620.15693532X-RAY DIFFRACTION99.65
5.13-29.450.22261400.19363592X-RAY DIFFRACTION99.36
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)
15.03304083178-1.047159788280.05855415312566.4526536288-1.631045889214.22863152167-0.040339445660.2426640821740.152575701634-0.219275005224-0.198729311556-0.6592322854420.05065333582930.866213293860.161048223690.2921138608320.0006715558986980.01929411733630.5426004582550.007749820891980.37495174900614.666761056614.81756787520.0366478038
24.283943909472.666494075992.894387653264.894574733774.136440849966.27116909081-0.3375659755680.6485944896860.148032276089-0.4843040288720.48181437766-0.223881179643-0.4695829065920.464273929839-0.07138555677040.284463140367-0.0339026013270.02080504066740.3215681229210.05904429221310.316613820709-2.8363759609315.0478015366.9163370067
32.306017065680.4139403360720.9464639025892.829988578410.9812803895183.669950201780.0891758857539-0.0270544423343-0.06295480651340.202132846846-0.2074990811610.3558917056860.474924456516-0.5292070953090.1167460805070.318726300956-0.07455662280840.03832518765930.3540694005390.03043072882460.323264049485-7.9735863380910.460553560714.131436405
48.436436501942.850595664670.1459800961392.034851863980.08772398913197.263543045940.270363868618-0.340737509975-0.4050262963290.177684559667-0.039921395702-0.976677740417-0.02007830272531.10278204635-0.2173060511250.3510495454310.0708815782534-0.03784537428660.661186068944-0.007410084314280.40781516962617.558284255110.357005137410.5043456314
52.01516249943-1.62898342002-1.536195800491.133889044652.358082446725.239128918280.3170197371561.140233556441.71531956499-0.757638253348-0.2319749730220.133316069948-0.6795242062851.06929027858-0.09830269740460.496207509011-0.0275711192613-0.04747516648780.735063227360.1658084260650.58857189284812.847788364317.64048753847.68207290332
63.6714734448-0.2502895309071.265748358352.806468025560.9025734361044.868996069730.10724851166-0.41525662247-0.1403179135970.421998486726-0.08615438571370.1572269989430.36835462469-0.268776505196-0.02782816628360.296506579883-0.01082893907080.0280796787580.328580552350.02292367495350.292520964605-1.4300655259111.087993638722.0473009276
75.67585627310.0692487741978-2.853330448923.957577810020.295290121188.998618354970.3870607578260.306507042141.0200889645-0.354773164289-0.13983907591-0.129072001718-1.335601076260.235874016454-0.2535220417060.412312845253-0.0204734566665-0.03113246652360.3285938306930.104791343830.6616619735-3.3039853117130.639082027915.063203941
87.69292315664-1.76444043956-4.252976311496.073330347992.940832574952.045653228240.299088483025-0.04625834222170.922962907612-0.25800672370.162095924263-0.290953167634-1.04896972660.101580739665-0.497449652450.399918544320.0189095912519-0.03863827318510.3406908492220.05294291862150.463902898531-11.15498118725.007332619714.8090253035
92.754420340230.311203943450.04942119297983.83245749063-0.2960951501712.03160786260.04011028065250.1223345358670.476971250015-0.394598413661-0.2361504212870.450050432191-0.090051060816-0.5102736915670.1684907083910.3956048308390.127115274071-0.02521492518530.7231721618970.04748705053040.523296709465-46.386140741629.621253899717.571667189
102.78279134272-2.049856286531.683920695189.56182004856-6.174718785346.67846320305-0.0991386647382-0.3439492287140.09311577523241.08869557790.3472073951060.616810296536-0.753730817949-0.581477188726-0.2288024434420.353959993670.03227756524820.05668543690230.401707774413-0.05401716714680.329364222534-30.490308485522.160750099530.4592935229
111.69043451244-0.198816946351-0.1708777465123.45330040579-1.577963278392.84449656925-0.02800541272140.161528466190.016228663461-0.269480744067-0.167123681439-0.3359136320050.5051563711050.221561717510.1546479610590.3509473206980.05808469571260.002952008191050.437523238424-0.004775963790530.315738481436-24.68059872816.318625288823.2044335733
124.74694722086-2.867642195590.650931375555.4133726655-0.7302735597591.6996098902-0.178118649011-0.693709333882-0.4840969867840.2968138405670.2867802627080.767032299049-0.102551688907-0.904335051087-0.1329221753940.4108584360810.0468702961342-0.03421384740280.722654546287-0.007746776620380.440775410012-47.704581916222.404748238526.77805494
134.59386796536-2.313766038260.7094954095774.67502960711-1.070962911772.76509455289-0.03919736852360.2019823386080.228999239232-0.0275428538213-0.02386845852580.3191422964210.0574918613778-0.6780314133080.05891862861880.2622198229510.002760389464310.01259215960890.547813377183-0.005358612128750.326548871217-37.482403714819.874024797921.2675718527
144.26983023671-0.752282860634-0.3669934820457.660786111520.7368715763884.744942077020.603001905790.687994233217-0.5657862334-1.43868332481-0.5133400726991.483242839211.0397354382-0.530219806044-0.07467188618730.604831754579-0.0643157481186-0.1277113823670.666487106091-0.01828990703590.582550268776-42.232324757512.712510862812.7876130709
155.07772037147-0.3905364247810.3038479685433.31237374558-1.923248741163.907930839010.08054475211240.5371141648870.586080469143-0.565895149118-0.0937904678676-0.0843046588599-0.0513029404164-0.1848071798470.02468361523180.3219792438650.08504343412820.05746538995950.4408273949960.05559447319720.344808129879-27.382617056625.475654090616.0866742572
166.133942521520.846210152474-1.90041170335.16425570567-1.883319997496.870786418420.166640562658-0.1613909115240.9719625592830.451229721861-0.0736793728251-0.125970684173-0.933948064198-0.014068164407-0.09984806932760.3843996122160.0776030316862-0.06521517006540.340953876176-0.01363257731330.457379698853-19.741592106227.557087819423.5467831678
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 8 through 26 )AA8 - 261 - 19
22chain 'A' and (resid 27 through 51 )AA27 - 5120 - 44
33chain 'A' and (resid 52 through 94 )AA52 - 9445 - 87
44chain 'A' and (resid 95 through 110 )AA95 - 11088 - 103
55chain 'A' and (resid 111 through 122 )AA111 - 122104 - 115
66chain 'A' and (resid 123 through 186 )AA123 - 186116 - 180
77chain 'A' and (resid 187 through 197 )AA187 - 197181 - 191
88chain 'A' and (resid 198 through 214 )AA198 - 214192 - 208
99chain 'B' and (resid 9 through 26 )BD9 - 261 - 18
1010chain 'B' and (resid 27 through 51 )BD27 - 5119 - 43
1111chain 'B' and (resid 52 through 85 )BD52 - 8544 - 77
1212chain 'B' and (resid 86 through 110 )BD86 - 11078 - 102
1313chain 'B' and (resid 111 through 150 )BD111 - 150103 - 142
1414chain 'B' and (resid 151 through 160 )BD151 - 160143 - 152
1515chain 'B' and (resid 161 through 197 )BD161 - 197153 - 189
1616chain 'B' and (resid 198 through 213 )BD198 - 213190 - 205

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