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- PDB-9nzl: Crystal structure of Yck2 with DJS-02-24-06 -

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Basic information

Entry
Database: PDB / ID: 9nzl
TitleCrystal structure of Yck2 with DJS-02-24-06
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
: / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.92 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 DJS-02-24-06
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)35,9115
Polymers35,3971
Non-polymers5144
Water6,810378
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)91.824, 91.824, 118.714
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-A1B7R / (4M)-4-[3-(5-methylpyridin-2-yl)-1H-pyrazol-4-yl]quinoline


Mass: 286.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H14N4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 54.8 %
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: Dec 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.92→29.97 Å / Num. obs: 28502 / % possible obs: 100 % / Redundancy: 4.2 % / Biso Wilson estimate: 26.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.67
Reflection shellResolution: 1.92→1.99 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 1.67 / Num. unique obs: 2849 / CC1/2: 0.663 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
PHENIXmodel building
DMmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→29.97 Å / SU ML: 0.226 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 22.3307
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1997 1475 5.18 %
Rwork0.1583 27026 -
obs0.1605 28501 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.99 Å2
Refinement stepCycle: LAST / Resolution: 1.92→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2493 0 33 378 2904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00572586
X-RAY DIFFRACTIONf_angle_d0.72693496
X-RAY DIFFRACTIONf_chiral_restr0.0489361
X-RAY DIFFRACTIONf_plane_restr0.0058456
X-RAY DIFFRACTIONf_dihedral_angle_d15.495990
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.980.33961340.24232442X-RAY DIFFRACTION99.81
1.98-2.050.28161240.20842495X-RAY DIFFRACTION100
2.05-2.140.22431360.17652466X-RAY DIFFRACTION100
2.14-2.230.19781250.172437X-RAY DIFFRACTION100
2.23-2.350.22371420.17792465X-RAY DIFFRACTION100
2.35-2.50.23891320.16542434X-RAY DIFFRACTION100
2.5-2.690.21451320.17132470X-RAY DIFFRACTION100
2.69-2.960.1921350.17392449X-RAY DIFFRACTION100
2.96-3.390.21561470.15562439X-RAY DIFFRACTION99.96
3.39-4.270.16791330.13592453X-RAY DIFFRACTION100
4.27-29.970.16381350.13332476X-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)
11.25394494408-1.03799406590.8318347493022.410391314080.005858325901620.865199924031-0.0472168883792-0.246017327162-0.4106652452080.577748401855-0.05953588939580.6283250054450.112144983992-0.470881882561-0.0009150419152160.404606509833-0.03837696927830.1165476345360.331683631149-0.0268687743440.45594864024223.0987323422-43.799197622913.3273503871
22.06433292109-0.346860056604-0.1418955968361.69619233031-0.22882838480.988910988598-0.07206315835440.0391523576901-0.455244663917-0.01420596172670.02031796659940.01402372838780.125901893449-0.242447117293-0.0031264504630.147213976261-0.02580989396150.004748831566610.236374596498-0.02570392668030.20177508058717.6854489665-30.22457544878.67379097742
32.716705280620.602056524291-0.62023116161.4316569448-0.03919142460911.13742769448-0.00408932156806-0.01374910331130.1196945698370.1037042812280.0151991433344-0.00403516437508-0.158713875725-0.1707842975610.002524837515660.1534707898840.0480452408621-0.01839898846730.22554895853-0.0004053465532790.15032059849715.4130066837-16.310080992110.9410878469
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 102 )37 - 1021 - 66
22chain 'A' and (resid 103 through 213 )103 - 21367 - 177
33chain 'A' and (resid 214 through 345 )214 - 345178 - 309

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