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- PDB-4l5b: Human dCK C4S-S74E mutant in complex with UDP and the DI-43 inhibitor -

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Basic information

Entry
Database: PDB / ID: 4l5b
TitleHuman dCK C4S-S74E mutant in complex with UDP and the DI-43 inhibitor
ComponentsDeoxycytidine kinase
Keywordstransferase/transferase inhibitor / phosphoryl transfer / phosphorylation / deoxycytidine kinase / transferase-transferase inhibitor complex
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
Chem-1UX / URIDINE-5'-DIPHOSPHATE / Deoxycytidine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsNomme, J. / Lavie, A.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Development of new deoxycytidine kinase inhibitors and noninvasive in vivo evaluation using positron emission tomography.
Authors: Murphy, J.M. / Armijo, A.L. / Nomme, J. / Lee, C.H. / Smith, Q.A. / Li, Z. / Campbell, D.O. / Liao, H.I. / Nathanson, D.A. / Austin, W.R. / Lee, J.T. / Darvish, R. / Wei, L. / Wang, J. / Su, ...Authors: Murphy, J.M. / Armijo, A.L. / Nomme, J. / Lee, C.H. / Smith, Q.A. / Li, Z. / Campbell, D.O. / Liao, H.I. / Nathanson, D.A. / Austin, W.R. / Lee, J.T. / Darvish, R. / Wei, L. / Wang, J. / Su, Y. / Damoiseaux, R. / Sadeghi, S. / Phelps, M.E. / Herschman, H.R. / Czernin, J. / Alexandrova, A.N. / Jung, M.E. / Lavie, A. / Radu, C.G.
History
DepositionJun 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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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)67,1636
Polymers65,4032
Non-polymers1,7604
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-30 kcal/mol
Surface area20430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.671, 68.671, 120.019
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Deoxycytidine kinase / dCK


Mass: 32701.627 Da / Num. of mol.: 2 / Fragment: Human deoxycytidine kinase / Mutation: C9S, C45S, C59S, S74E, 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) / Strain (production host): BL21 C41 / References: UniProt: P27707, deoxycytidine kinase
#2: Chemical ChemComp-1UX / 1-[5-(4-{[(4,6-diaminopyrimidin-2-yl)sulfanyl]methyl}-5-propyl-1,3-thiazol-2-yl)-2-methoxyphenoxy]-2-methylpropan-2-ol


Mass: 475.627 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H29N5O3S2
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.16 Å3/Da / Density % sol: 43.14 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.9-1.5 M trisodium citrate dehydrate, 25 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 8, 2012
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.511
11-H, K, -L20.489
ReflectionResolution: 1.94→20 Å / Num. all: 40954 / Num. obs: 40954 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.05
Reflection shellResolution: 1.94→2.05 Å / Rmerge(I) obs: 0.718 / Mean I/σ(I) obs: 2.05 / Num. unique all: 6489 / % possible all: 98.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.7.0032refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3QEN

3qen


Resolution: 1.94→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.576 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 1964 4.9 %RANDOM
Rwork0.18781 ---
obs0.19001 38256 97.46 %-
all-38256 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.095 Å2
Baniso -1Baniso -2Baniso -3
1--4.8 Å20 Å20 Å2
2---4.8 Å20 Å2
3---9.6 Å2
Refinement stepCycle: LAST / Resolution: 1.94→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3835 0 114 75 4024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.024075
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.9815536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5515469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.85624.483203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.0715716
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7041522
X-RAY DIFFRACTIONr_chiral_restr0.1060.2583
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213080
LS refinement shellResolution: 1.937→1.987 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 148 -
Rwork0.223 2777 -
obs--96.28 %

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