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- PDB-3kfx: Human dCK complex with 5-Me dC and ADP -

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Basic information

Entry
Database: PDB / ID: 3kfx
TitleHuman dCK complex with 5-Me dC and ADP
ComponentsDeoxycytidine kinase
KeywordsTRANSFERASE / Human dCK / Nucleotide Kinase / P-Loop / 5-Me dC / ATP-binding / Kinase / Nucleotide-binding / Nucleus / Phosphoprotein
Function / homology
Function and homology information


deoxycytidine kinase / 2'-deoxyadenosine kinase / deoxyguanosine kinase / dAMP salvage / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / deoxyguanosine kinase activity / deoxyadenosine kinase activity / Pyrimidine salvage / cytidine kinase activity ...deoxycytidine kinase / 2'-deoxyadenosine kinase / deoxyguanosine kinase / dAMP salvage / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / deoxyguanosine kinase activity / deoxyadenosine kinase activity / Pyrimidine salvage / cytidine kinase activity / pyrimidine nucleotide metabolic process / Purine salvage / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding / cytosol / cytoplasm
Similarity search - Function
Deoxynucleoside kinase / : / Deoxynucleoside kinase domain / Deoxynucleoside kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 5-METHYL-2'-DEOXYCYTIDINE / Deoxycytidine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsHazra, S. / Lavie, A.
CitationJournal: Biochemistry / Year: 2010
Title: Structural and kinetic characterization of human deoxycytidine kinase variants able to phosphorylate 5-substituted deoxycytidine and thymidine analogues .
Authors: Hazra, S. / Ort, S. / Konrad, M. / Lavie, A.
History
DepositionOct 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deoxycytidine kinase
B: Deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4826
Polymers65,1452
Non-polymers1,3374
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-22.2 kcal/mol
Surface area20530 Å2
MethodPISA
2
A: Deoxycytidine kinase
B: Deoxycytidine kinase
hetero molecules

A: Deoxycytidine kinase
B: Deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,96412
Polymers130,2904
Non-polymers2,6748
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area7000 Å2
ΔGint-55.8 kcal/mol
Surface area39350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.740, 132.950, 156.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Deoxycytidine kinase / dCK


Mass: 32572.510 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCK / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P27707, deoxycytidine kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MCY / 5-METHYL-2'-DEOXYCYTIDINE


Type: DNA linking / Mass: 241.244 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N3O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.8 M Sodium citrate, pH 7.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.96→30 Å / Num. obs: 39888 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.193 / Rsym value: 0.23 / Net I/σ(I): 23
Reflection shellResolution: 1.96→2.08 Å / Mean I/σ(I) obs: 4.1 / % possible all: 95.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.99 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23956 3823 10 %RANDOM
Rwork0.18837 ---
obs0.19339 34560 95.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.039 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.96→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3850 0 88 253 4191
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224038
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.975495
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8445468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.81924.293198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.69815674
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1481522
X-RAY DIFFRACTIONr_chiral_restr0.0990.2595
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023055
X-RAY DIFFRACTIONr_nbd_refined0.2020.21882
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22755
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2286
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2380.228
X-RAY DIFFRACTIONr_mcbond_it0.8851.52399
X-RAY DIFFRACTIONr_mcangle_it1.52323784
X-RAY DIFFRACTIONr_scbond_it2.17131921
X-RAY DIFFRACTIONr_scangle_it3.2554.51711
LS refinement shellResolution: 1.96→2.01 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 261 -
Rwork0.265 2315 -
obs--88.61 %

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