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- PDB-2no9: The structure of deoxycytidine kinase complexed with troxacitabin... -

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Basic information

Entry
Database: PDB / ID: 2no9
TitleThe structure of deoxycytidine kinase complexed with troxacitabine and ADP.
Componentsdeoxycytidine kinase
KeywordsTRANSFERASE / dCK / troxacitabine / human deoxycytidine kinase / L-dC / enantiomer / anticancer
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 / cytoplasm / cytosol
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 / Chem-LTT / Deoxycytidine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSabini, E. / Lavie, A.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: Structural basis for activation of the therapeutic L-nucleoside analogs 3TC and troxacitabine by human deoxycytidine kinase.
Authors: Sabini, E. / Hazra, S. / Konrad, M. / Burley, S.K. / Lavie, A.
History
DepositionOct 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Category: citation_author / struct_site
Item: _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id ..._citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)66,6006
Polymers65,3192
Non-polymers1,2814
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-15 kcal/mol
Surface area20430 Å2
MethodPISA
2
A: deoxycytidine kinase
hetero molecules

A: deoxycytidine kinase
hetero molecules

B: deoxycytidine kinase
hetero molecules

B: deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,20012
Polymers130,6384
Non-polymers2,5628
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_545x+1/2,y-1/2,z1
crystal symmetry operation8_566x+1/2,-y+3/2,-z+11
Buried area9980 Å2
ΔGint-25 kcal/mol
Surface area40870 Å2
MethodPISA
3
A: deoxycytidine kinase
B: deoxycytidine kinase
hetero molecules

A: deoxycytidine kinase
B: deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,20012
Polymers130,6384
Non-polymers2,5628
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area11750 Å2
ΔGint-41 kcal/mol
Surface area39100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.850, 134.460, 155.340
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: 32659.588 Da / Num. of mol.: 2 / Mutation: C9S,C45S,C59S,C146S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCK / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / 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-LTT / 4-AMINO-1-[(2S,4S)-2-(HYDROXYMETHYL)-1,3-DIOXOLAN-4-YL]PYRIMIDIN-2(1H)-ONE / (-)-L-2',3'-DIDEOXY-3'-OXACYTIDINE / TROXACITABINE / TROXATYL


Mass: 213.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11N3O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.26 Å3/Da / Density % sol: 45.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Reservoir containing 0.95-1.5M trisodium citrate dihydrate and 100mM HEPES, pH 7.5., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 20, 2005 / Details: mirrors
RadiationMonochromator: Rosenbaum-Rock monochromator high-resolution double-crystal Si (111) sagittal focusing, Rosenbaum-Rock vertical
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. all: 30620 / Num. obs: 30536 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 34 Å2 / Rsym value: 0.099 / Net I/σ(I): 10.9
Reflection shellResolution: 2.15→2.2 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 2026 / Rsym value: 0.511 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P5Z

1p5z


Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.467 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.258 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25493 3070 10.1 %RANDOM
Rwork0.19501 ---
obs0.20111 27466 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2---0.7 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3850 0 84 79 4013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224033
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.975483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0925466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.47324.455202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.24515681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7461522
X-RAY DIFFRACTIONr_chiral_restr0.1120.2590
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023067
X-RAY DIFFRACTIONr_nbd_refined0.2090.21722
X-RAY DIFFRACTIONr_nbtor_refined0.3140.22761
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2219
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2910.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.26
X-RAY DIFFRACTIONr_mcbond_it1.0771.52402
X-RAY DIFFRACTIONr_mcangle_it1.79323770
X-RAY DIFFRACTIONr_scbond_it2.60831923
X-RAY DIFFRACTIONr_scangle_it3.8514.51713
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 235 -
Rwork0.216 2005 -
obs--100 %

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