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- PDB-5j0a: Crystal structure of PDZ-binding kinase -

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Basic information

Entry
Database: PDB / ID: 5j0a
TitleCrystal structure of PDZ-binding kinase
Components(Lymphokine-activated killer T-cell-originated protein kinase) x 2
KeywordsTRANSFERASE / Protein kinase
Function / homology
Function and homology information


protein serine/threonine kinase activity => GO:0004674 / mitogen-activated protein kinase kinase / negative regulation of stress-activated MAPK cascade / MAP kinase kinase activity / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / transmembrane receptor protein tyrosine kinase activity / negative regulation of protein phosphorylation / negative regulation of inflammatory response / cellular response to UV / mitotic cell cycle ...protein serine/threonine kinase activity => GO:0004674 / mitogen-activated protein kinase kinase / negative regulation of stress-activated MAPK cascade / MAP kinase kinase activity / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / transmembrane receptor protein tyrosine kinase activity / negative regulation of protein phosphorylation / negative regulation of inflammatory response / cellular response to UV / mitotic cell cycle / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus
Similarity search - Function
TOPK, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
4'-HYDROXYCINNAMIC ACID / Lymphokine-activated killer T-cell-originated protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.74 Å
AuthorsZou, Q.W. / Zhou, H. / Yang, X.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: The crystal structure of an inactive dimer of PDZ-binding kinase
Authors: Dong, C. / Tang, X. / Xie, Y. / Zou, Q. / Yang, X. / Zhou, H.
History
DepositionMar 28, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lymphokine-activated killer T-cell-originated protein kinase
B: Lymphokine-activated killer T-cell-originated protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,24816
Polymers67,6312
Non-polymers1,61714
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12210 Å2
ΔGint-188 kcal/mol
Surface area27550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.558, 97.905, 162.835
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lymphokine-activated killer T-cell-originated protein kinase / Cancer/testis antigen 84 / CT84 / MAPKK-like protein kinase / Nori-3 / PDZ-binding kinase / ...Cancer/testis antigen 84 / CT84 / MAPKK-like protein kinase / Nori-3 / PDZ-binding kinase / Spermatogenesis-related protein kinase / SPK / T-LAK cell-originated protein kinase


Mass: 33629.012 Da / Num. of mol.: 1 / Fragment: UNP residues 23-320 / Mutation: T198E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PBK, TOPK / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q96KB5, mitogen-activated protein kinase kinase
#2: Protein Lymphokine-activated killer T-cell-originated protein kinase / Cancer/testis antigen 84 / CT84 / MAPKK-like protein kinase / Nori-3 / PDZ-binding kinase / ...Cancer/testis antigen 84 / CT84 / MAPKK-like protein kinase / Nori-3 / PDZ-binding kinase / Spermatogenesis-related protein kinase / SPK / T-LAK cell-originated protein kinase


Mass: 34001.492 Da / Num. of mol.: 1 / Fragment: UNP residues 19-319 / Mutation: T198E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PBK, TOPK / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q96KB5, mitogen-activated protein kinase kinase
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-HC4 / 4'-HYDROXYCINNAMIC ACID / PARA-COUMARIC ACID


Mass: 164.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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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: 4.46 Å3/Da / Density % sol: 72.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulfate, 2.0 M ammonium sulfate, 0.1 M CAPS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.74→32.76 Å / Num. obs: 32541 / Biso Wilson estimate: 28.9 Å2
Reflection shellResolution: 2.74→2.87 Å

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.74→32.76 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1070756.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1580 5.1 %RANDOM
Rwork0.222 ---
obs0.222 31109 95.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.4405 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 71.1 Å2
Baniso -1Baniso -2Baniso -3
1--5.61 Å20 Å20 Å2
2--20.98 Å20 Å2
3----15.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.68 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2.74→32.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2380 0 48 164 2592
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.42
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.521.5
X-RAY DIFFRACTIONc_mcangle_it2.732
X-RAY DIFFRACTIONc_scbond_it1.92
X-RAY DIFFRACTIONc_scangle_it3.092.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.74→2.87 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.424 172 5.8 %
Rwork0.355 2769 -
obs--53 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR/protein_rep.paramCNS_TOPPAR/protein.top
X-RAY DIFFRACTION2CNS_TOPPAR/water_rep.paramCNS_TOPPAR/water.top
X-RAY DIFFRACTION3./so4.par./so4.top
X-RAY DIFFRACTION4./coma.par./coma.top

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