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- PDB-9nzk: Crystal structure of Yck2 with LY364947 -

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Basic information

Entry
Database: PDB / ID: 9nzk
TitleCrystal structure of Yck2 with LY364947
Componentsnon-specific serine/threonine protein kinase
KeywordsTRANSFERASE/INHIBITOR / YCK2 / KINASE / KINASE INHIBITOR / STRUCTURAL GENOMICS / NIAID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES / Center for Structural Biology of Infectious Diseases / CSBID / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


filamentous growth / 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
4-(3-PYRIDIN-2-YL-1H-PYRAZOL-4-YL)QUINOLINE / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsStogios, P.J. / Shirley, D. / Cowen, L.E. / Willson, T. / 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) United States
CitationJournal: To Be Published
Title: Crystal structure of Yck2 with LY364947
Authors: Stogios, P.J.
History
DepositionApr 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 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: non-specific serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7404
Polymers35,3971
Non-polymers3433
Water6,431357
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)91.532, 91.532, 118.824
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-PY1 / 4-(3-PYRIDIN-2-YL-1H-PYRAZOL-4-YL)QUINOLINE


Mass: 272.304 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H12N4 / 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.: 357 / 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: 2.71 Å3/Da / Density % sol: 54.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Tris pH 8, 25 mM Magnesium chloride, 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5418 Å
DetectorType: DECTRIS EIGER R 1M / Detector: PIXEL / Date: Nov 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→29.95 Å / Num. obs: 40815 / % possible obs: 99.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 26.51 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.25
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 0.48 / Num. unique obs: 4046 / CC1/2: 0.445 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→29.95 Å / SU ML: 0.243 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.8367
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2111 1949 4.78 %
Rwork0.1743 38794 -
obs0.1761 40743 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.97 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2469 0 23 357 2849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112552
X-RAY DIFFRACTIONf_angle_d1.11193448
X-RAY DIFFRACTIONf_chiral_restr0.0742358
X-RAY DIFFRACTIONf_plane_restr0.0096451
X-RAY DIFFRACTIONf_dihedral_angle_d14.4664978
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.39081360.35532708X-RAY DIFFRACTION96.21
1.74-1.790.32411400.32832771X-RAY DIFFRACTION99.73
1.79-1.840.32361280.27672776X-RAY DIFFRACTION99.97
1.84-1.90.27141470.22882769X-RAY DIFFRACTION100
1.9-1.970.27511230.23642786X-RAY DIFFRACTION100
1.97-2.050.26181390.21662783X-RAY DIFFRACTION100
2.05-2.140.23411440.17772797X-RAY DIFFRACTION99.93
2.14-2.250.19571340.16082750X-RAY DIFFRACTION99.86
2.25-2.40.22241420.18382759X-RAY DIFFRACTION100
2.4-2.580.20661390.16932779X-RAY DIFFRACTION100
2.58-2.840.23361480.18952773X-RAY DIFFRACTION100
2.84-3.250.22741350.16862801X-RAY DIFFRACTION99.97
3.25-4.090.17821550.14712751X-RAY DIFFRACTION100
4.09-29.950.1671390.13582791X-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)
16.43281262013-1.216318372410.8116778218132.869311000750.8917232152323.72742670758-0.2206025826940.592056357275-0.0330393187444-1.310369055650.2371138449820.0811303794621-0.0259868202167-0.7939143390960.004989995933660.589801020119-0.139933413621-0.1574944475660.3861182833580.07800919478940.38910663920725.853893306-8.13292834568-16.3542555249
22.711839540110.5810852401150.3058793313382.36452106758-0.1529014433661.14660494517-0.116082914561-0.007151184426990.5388771360040.008650111595450.0331287301730.163320018699-0.210644030194-0.22755756660.05931322167990.1645828327530.0175517286519-0.007968468381270.229747240059-0.01404796428430.2056216064116.337663772-22.2778722529-7.8803627815
33.44443440057-0.5436267432720.8218599864621.70821785553-0.08094196459491.46855279293-0.0308713594496-0.00832114799723-0.221822479737-0.09681401167750.06211039364840.08774562288720.155776583385-0.220020494883-0.03212412805480.171746409976-0.05755185323780.02388798837210.21652894060.001339439350620.16203772727316.371600322-37.656919032-9.14414656399
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 83 )37 - 831 - 47
22chain 'A' and (resid 84 through 228 )84 - 22848 - 192
33chain 'A' and (resid 229 through 342 )229 - 342193 - 306

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