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- PDB-6u6a: Crystal structure of Yck2 from Candida albicans in complex with k... -

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Basic information

Entry
Database: PDB / ID: 6u6a
TitleCrystal structure of Yck2 from Candida albicans in complex with kinase inhibitor GW461484A
ComponentsSerine/threonine protein kinaseSerine/threonine-specific protein kinase
KeywordsTRANSFERASE/TRANSFERASE Inhibitor / casein kinase 1 / Yck2 / kinase / kinase inhibitor / structural genomics / center for structural genomics of infectious diseases / niaid / national institute of allergy and infectious diseases / TRANSFERASE / TRANSFERASE-TRANSFERASE Inhibitor complex
Function / homology
Function and homology information


regulation of single-species biofilm formation / regulation of cell wall organization or biogenesis / hyphal growth / regulation of filamentous growth / biological process involved in interaction with host / endocytosis / extracellular vesicle / peptidyl-serine phosphorylation / protein serine/threonine kinase activity / signal transduction ...regulation of single-species biofilm formation / regulation of cell wall organization or biogenesis / hyphal growth / regulation of filamentous growth / biological process involved in interaction with host / endocytosis / extracellular vesicle / peptidyl-serine phosphorylation / protein serine/threonine kinase activity / signal transduction / ATP binding / nucleus / plasma membrane
Similarity search - Function
Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. ...Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-Q0J / Serine/threonine protein kinase
Similarity search - Component
Biological speciesCandida albicans SC5314 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsStogios, P.J. / Evdokimova, E. / Di Leo, R. / Chang, C. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: Cell Chem Biol / Year: 2020
Title: Overcoming Fungal Echinocandin Resistance through Inhibition of the Non-essential Stress Kinase Yck2.
Authors: Caplan, T. / Lorente-Macias, A. / Stogios, P.J. / Evdokimova, E. / Hyde, S. / Wellington, M.A. / Liston, S. / Iyer, K.R. / Puumala, E. / Shekhar-Guturja, T. / Robbins, N. / Savchenko, A. / ...Authors: Caplan, T. / Lorente-Macias, A. / Stogios, P.J. / Evdokimova, E. / Hyde, S. / Wellington, M.A. / Liston, S. / Iyer, K.R. / Puumala, E. / Shekhar-Guturja, T. / Robbins, N. / Savchenko, A. / Krysan, D.J. / Whitesell, L. / Zuercher, W.J. / Cowen, L.E.
History
DepositionAug 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 11, 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

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Assembly

Deposited unit
A: Serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8934
Polymers35,3971
Non-polymers4953
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.563, 91.563, 119.624
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11A-609-

HOH

21A-616-

HOH

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Components

#1: Protein Serine/threonine protein kinase / Serine/threonine-specific protein kinase


Mass: 35397.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans SC5314 (yeast) / Strain: SC5314 / ATCC MYA-2876 / Gene: YCK2, orf19.7001, CAALFM_C305650WA / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Gold / References: UniProt: A0A1D8PKB4
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-Q0J / 2-(4-fluorophenyl)-6-methyl-3-(pyridin-4-yl)pyrazolo[1,5-a]pyridine


Mass: 303.333 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H14FN3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.75 Å3/Da / Density % sol: 55.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris pH 8, 25 mM magnesium chloride, 22% (w/v) PEG3350, 1 mM GW461484A soak

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 13621 / % possible obs: 98.8 % / Redundancy: 7 % / Biso Wilson estimate: 35.93 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.033 / Net I/σ(I): 23.16
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 2.13 / Num. unique obs: 602 / CC1/2: 0.969 / Rpim(I) all: 0.887 / % possible all: 88.8

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Processing

Software
NameVersionClassification
PHENIX1.15_3448refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X18

5x18


Resolution: 2.45→37.63 Å / SU ML: 0.2432 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 24.2904
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2122 642 5.08 %RANDOM
Rwork0.1627 11984 --
obs0.1653 12626 91.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.13 Å2
Refinement stepCycle: LAST / Resolution: 2.45→37.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2469 0 33 116 2618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722562
X-RAY DIFFRACTIONf_angle_d1.0393464
X-RAY DIFFRACTIONf_chiral_restr0.0529358
X-RAY DIFFRACTIONf_plane_restr0.006451
X-RAY DIFFRACTIONf_dihedral_angle_d23.0605956
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.640.2976840.22711719X-RAY DIFFRACTION65.21
2.64-2.90.25261290.20452446X-RAY DIFFRACTION93.09
2.9-3.320.2541490.18442598X-RAY DIFFRACTION99.89
3.32-4.190.18461420.14312615X-RAY DIFFRACTION99.96
4.19-37.630.18471380.14342606X-RAY DIFFRACTION99.82
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)
16.02880227423-2.27885257766-1.39112054154.081910610222.2459347043.712542045641.16110763489-1.27920399041-0.002651097462571.58831206143-1.17974351141-0.1090718208461.469482598830.4816417369620.0855383979120.71002324312-0.39089121056-0.03999828103080.575650083797-0.04795813431490.3202176262424.0545085921-6.023155840118.6976821434
21.711188729810.392539344534-0.5898093826190.9603155948971.29622155693.453027364520.641097578086-0.84769158171-0.002142774554321.03726783735-0.887293841947-0.9093991704080.3178733621540.7147989912010.201229717120.364810292147-0.121336243775-0.2344277799340.5135383172650.1946467440050.568502768726.9051017552-9.6740718828716.1028930147
38.319971505071.95944860937-0.5073902244584.92636020402-0.3060300755432.00530115576-0.209120350686-0.3304448541020.07279003337460.0685976219817-0.100012209519-0.7953416025250.08294673468570.4177407948640.2439265933780.2055942167020.0646535469534-0.01019228551230.1984659214990.03473046570190.30398539749719.8904543621-15.229779932911.2093424039
44.76613257053-1.170123177240.1147004172614.61380556710.8095323180632.09433036280.1284372146490.1853030497810.333381223728-0.143340674186-0.0493384059173-0.6686668921120.09827022962080.43359253515-0.02910690768770.1833109868080.0627754167740.02074300625720.1902011474430.009816643211570.22544774968517.6035835425-25.82871292315.64763464013
54.18545702037-3.49501644105-2.42843601763.029994726322.142164207171.48977393009-0.174603880397-0.2251335453990.5380108191080.6182312476830.259427901929-0.8462035783080.8621469589280.476071012524-0.1718891259920.5212610966240.185996740863-0.008625795496790.2885095250270.05416714757490.40423714580917.2346565644-37.181669911715.5384715534
64.69005801445-0.9247407384990.6641805000413.44688983185-0.6310032036952.952574798110.0560698735646-0.175156301652-0.192632944934-0.006638207644680.03736833915080.2039506585810.41364727197-0.0418276606926-0.07450267882950.2930376187460.002951582818460.0005458320119340.112830746914-0.04259284840270.17184932395.0568402032-31.069360210810.2850412542
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 37 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 83 )
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 136 )
4X-RAY DIFFRACTION4chain 'A' and (resid 137 through 209 )
5X-RAY DIFFRACTION5chain 'A' and (resid 210 through 228 )
6X-RAY DIFFRACTION6chain 'A' and (resid 229 through 342 )

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