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- PDB-2no0: C4S dCK variant of dCK in complex with gemcitabine+ADP -

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Basic information

Entry
Database: PDB / ID: 2no0
TitleC4S dCK variant of dCK in complex with gemcitabine+ADP
ComponentsDeoxycytidine kinase
KeywordsTRANSFERASE / dCK / gemcitabine / human deoxycytidine kinase
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 / GEMCITABINE / Deoxycytidine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSabini, E. / Hazra, S. / Konrad, M. / Burley, S.K. / Lavie, A.
CitationJournal: J.Med.Chem. / Year: 2007
Title: Nonenantioselectivity Property of Human Deoxycytidine Kinase Explained by Structures of the Enzyme in Complex with l- and d-Nucleosides.
Authors: Sabini, E. / Hazra, S. / Konrad, M. / Lavie, A.
History
DepositionOct 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.4Feb 3, 2021Group: Derived calculations / Structure summary / Category: audit_author / struct_site
Item: _audit_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id ..._audit_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 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 1.6Aug 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)66,7006
Polymers65,3192
Non-polymers1,3814
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-21 kcal/mol
Surface area20330 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)133,40012
Polymers130,6384
Non-polymers2,7628
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 area10390 Å2
ΔGint-33 kcal/mol
Surface area40730 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)133,40012
Polymers130,6384
Non-polymers2,7628
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area12250 Å2
ΔGint-53 kcal/mol
Surface area38870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.300, 132.400, 157.300
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-GEO / GEMCITABINE / 2',2'-DIFLUORODEOXYCYTIDINE


Mass: 263.198 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11F2N3O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
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: Feb 8, 2006 / 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: 1.8→30 Å / Num. all: 51063 / Num. obs: 50852 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Rsym value: 0.074 / Net I/σ(I): 16.6
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 7368 / Rsym value: 0.363

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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: 1.8→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.338 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21141 5123 10.1 %RANDOM
Rwork0.17254 ---
obs0.17655 45728 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.547 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2---0.22 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3884 0 90 267 4241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224074
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.9725534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2785462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29124.593209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08715708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0741522
X-RAY DIFFRACTIONr_chiral_restr0.1010.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023087
X-RAY DIFFRACTIONr_nbd_refined0.2010.21856
X-RAY DIFFRACTIONr_nbtor_refined0.310.22792
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2299
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.219
X-RAY DIFFRACTIONr_mcbond_it1.1341.52398
X-RAY DIFFRACTIONr_mcangle_it1.79523769
X-RAY DIFFRACTIONr_scbond_it2.77531971
X-RAY DIFFRACTIONr_scangle_it4.0164.51763
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 336 -
Rwork0.22 3193 -
obs--95.9 %

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