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- PDB-9edx: Crystal structure of Yck2 from Candida albicans in complex with i... -

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Basic information

Entry
Database: PDB / ID: 9edx
TitleCrystal structure of Yck2 from Candida albicans in complex with inhibitor 2a: 2-(4-fluorophenyl)-3-(pyridin-4-yl)pyrazolo[1,5-a]pyridine-6-carbonitrile
Componentsnon-specific serine/threonine protein kinase
KeywordsTRANSFERASE/INHIBITOR / YCK2 / KINASE / KINASE INHIBITOR / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL BIOLOY OF INFECTIOUS DISEASES / NIAID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES / TRANSFERASE / TRANSFERASE-INHIBITOR complex / Center for Structural Biology of Infectious Diseases / CSBID
Function / homology
Function and homology information


non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / ATP binding
Similarity search - Function
: / 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
Similarity search - Domain/homology
: / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsStogios, P.J. / Whitesell, L. / Cowen, L.E. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00035 United States
CitationJournal: To Be Published
Title: Crystal structure of Yck2 from Candida albicans in complex with inhibitor 2a: 2-(4-fluorophenyl)-3-(pyridin-4-yl)pyrazolo[1,5-a]pyridine-6-carbonitrile
Authors: Stogios, P.J.
History
DepositionNov 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: non-specific serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7824
Polymers35,3971
Non-polymers3853
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.710, 91.710, 118.950
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

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Components

#1: Protein non-specific serine/threonine protein kinase


Mass: 35397.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: FOB64_000203 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): LOBSTR
References: UniProt: A0A8H6C375, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-A1BIO / 2-(4-fluorophenyl)-3-(pyridin-4-yl)pyrazolo[1,5-a]pyridine-6-carbonitrile


Mass: 314.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H11FN4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.72 Å3/Da / Density % sol: 54.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris pH 8, 25 mM Magnesium chloride, 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.18077 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18077 Å / Relative weight: 1
ReflectionResolution: 2.03→29.11 Å / Num. obs: 24095 / % possible obs: 100 % / Redundancy: 10.2 % / Biso Wilson estimate: 50.23 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.029 / Net I/σ(I): 19.2
Reflection shellResolution: 2.03→2.08 Å / Redundancy: 10.4 % / Rmerge(I) obs: 2.138 / Mean I/σ(I) obs: 1 / Num. unique obs: 1774 / CC1/2: 0.439 / Rpim(I) all: 1.044 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→29.11 Å / SU ML: 0.3133 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 34.0845
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2386 1205 5 %RANDOM
Rwork0.2156 22890 --
obs0.2167 24095 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.9 Å2
Refinement stepCycle: LAST / Resolution: 2.03→29.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2469 0 26 77 2572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00292555
X-RAY DIFFRACTIONf_angle_d0.51343453
X-RAY DIFFRACTIONf_chiral_restr0.0385358
X-RAY DIFFRACTIONf_plane_restr0.0055451
X-RAY DIFFRACTIONf_dihedral_angle_d13.6986956
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.110.34541670.3562507X-RAY DIFFRACTION100
2.11-2.210.34821610.30172542X-RAY DIFFRACTION100
2.21-2.320.3139830.29092550X-RAY DIFFRACTION99.96
2.32-2.470.24611140.24662567X-RAY DIFFRACTION100
2.47-2.660.27271490.25682530X-RAY DIFFRACTION100
2.66-2.930.29961620.26472505X-RAY DIFFRACTION100
2.93-3.350.24071290.23462552X-RAY DIFFRACTION100
3.35-4.220.2354940.1922594X-RAY DIFFRACTION100
4.22-29.110.19981460.18292543X-RAY DIFFRACTION100
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)
15.332234300022.43188644994-1.645447765214.94315046169-0.2341286767863.48210880363-0.2277385871110.5844273269370.343408772109-0.6138934938220.08949441928570.913757006786-0.494584375259-0.7216596065830.1221060541030.5458752786610.127653958849-0.1525665472890.515284839175-0.06801637979690.83044867667523.1220312988-8.46930253796-12.6548766363
26.35279825698-1.87222638818-1.301242078334.56671201552-0.2259873236291.749072681790.09915264567310.05175488503890.6301154933650.1278282666140.00931575373839-0.0487268156773-0.264675812905-0.263406250402-0.1123140007690.348340927372-0.006241018652540.02442234700470.4410600701620.0008355921791680.45254401493416.9110316393-25.7542587425-6.83515101095
34.04261246844-1.215763129330.08497483160533.16009749454-0.1081046812482.592321484930.0724309797273-0.037663682825-0.285212990035-0.126994207766-0.08856641245240.1150559779220.186885925241-0.2910783033030.008276191259050.319823397877-0.06673270128550.01330416647170.402095612922-0.003834149355470.34119685011414.9578557845-36.881281275-9.67536819714
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 37 through 118 )37 - 1181 - 82
22chain 'A' and (resid 119 through 213 )119 - 21383 - 177
33chain 'A' and (resid 214 through 342 )214 - 342178 - 306

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