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- PDB-4jlj: Human dCK C4S-S74E mutant in complex with UDP and the F2.1.1 inhi... -

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Basic information

Entry
Database: PDB / ID: 4jlj
TitleHuman dCK C4S-S74E mutant in complex with UDP and the F2.1.1 inhibitor (2-[({2-[3-(2-FLUOROETHOXY)-4-METHOXYPHENYL]-1,3-THIAZOL-4-YL}METHYL)SULFANYL]PYRIMIDINE-4,6-DIAMINE)
ComponentsDeoxycytidine kinase
Keywordstransferase/transferase inhibitor / phosphoryl transfer / phosphorylation / 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-1NM / URIDINE-5'-DIPHOSPHATE / Deoxycytidine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNomme, J. / Lavie, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural characterization of new deoxycytidine kinase inhibitors rationalizes the affinity-determining moieties of the molecules.
Authors: Nomme, J. / Murphy, J.M. / Su, Y. / Sansone, N.D. / Armijo, A.L. / Olson, S.T. / Radu, C. / Lavie, A.
History
DepositionMar 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: 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)67,8428
Polymers65,4032
Non-polymers2,4386
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-28 kcal/mol
Surface area21030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.998, 68.998, 123.180
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 / 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 DE3 C41 / References: UniProt: P27707, deoxycytidine kinase
#2: Chemical
ChemComp-1NM / 2-[({2-[3-(2-fluoroethoxy)-4-methoxyphenyl]-1,3-thiazol-4-yl}methyl)sulfanyl]pyrimidine-4,6-diamine


Mass: 407.486 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H18FN5O2S2
#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.: 119 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.13 %
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: Jan 31, 2013
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, L10.507
11-H, K, -L20.493
ReflectionResolution: 0→30 Å / Num. all: 38798 / Num. obs: 38798 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.99
Reflection shellResolution: 2→2.12 Å / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 2.3 / % possible all: 98.3

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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: 2→26.04 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.122 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23014 1993 5.2 %RANDOM
Rwork0.18426 ---
all0.18658 38798 --
obs0.18658 36331 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.66 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å20 Å20 Å2
2--1.93 Å20 Å2
3----3.86 Å2
Refinement stepCycle: LAST / Resolution: 2→26.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3860 0 158 119 4137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.024155
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.9925644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4045477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.06824.612206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.77615720
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1991522
X-RAY DIFFRACTIONr_chiral_restr0.1030.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213160
LS refinement shellResolution: 1.995→2.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 162 -
Rwork0.206 2615 -
obs--95.96 %

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