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- PDB-7zi6: Crystal structure of dCK C4S-S74E mutant in complex with UDP and ... -

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Basic information

Entry
Database: PDB / ID: 7zi6
TitleCrystal structure of dCK C4S-S74E mutant in complex with UDP and the OR0325 inhibitor
ComponentsDeoxycytidine kinase
KeywordsTRANSFERASE / Inhibitor
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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-JAQ / URIDINE-5'-DIPHOSPHATE / Deoxycytidine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSaez-Ayala, M. / Ben-Yaala, K. / Betzi, S. / Rebuffet, E. / Morelli, X.
Funding support France, 1items
OrganizationGrant numberCountry
Fondation ARCSL220130606659 France
CitationJournal: Nat Commun / Year: 2023
Title: From a drug repositioning to a structure-based drug design approach to tackle acute lymphoblastic leukemia.
Authors: Saez-Ayala, M. / Hoffer, L. / Abel, S. / Ben Yaala, K. / Sicard, B. / Andrieu, G.P. / Latiri, M. / Davison, E.K. / Ciufolini, M.A. / Bremond, P. / Rebuffet, E. / Roche, P. / Derviaux, C. / ...Authors: Saez-Ayala, M. / Hoffer, L. / Abel, S. / Ben Yaala, K. / Sicard, B. / Andrieu, G.P. / Latiri, M. / Davison, E.K. / Ciufolini, M.A. / Bremond, P. / Rebuffet, E. / Roche, P. / Derviaux, C. / Voisset, E. / Montersino, C. / Castellano, R. / Collette, Y. / Asnafi, V. / Betzi, S. / Dubreuil, P. / Combes, S. / Morelli, X.
History
DepositionApr 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6144
Polymers32,7021
Non-polymers9133
Water75742
1
A: Deoxycytidine kinase
hetero molecules

A: Deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2298
Polymers65,4032
Non-polymers1,8266
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area4130 Å2
ΔGint-52 kcal/mol
Surface area21150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.629, 68.629, 122.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Deoxycytidine kinase / dCK / Deoxyadenosine kinase / Deoxyguanosine kinase


Mass: 32701.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCK / Production host: Escherichia coli (E. coli)
References: UniProt: P27707, deoxycytidine kinase, 2'-deoxyadenosine kinase, deoxyguanosine kinase
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-JAQ / 4-(4-azanylpyrimidin-2-yl)-N-[2-methyl-5-[4-[2-(4-methylpiperazin-1-yl)ethyl]phenyl]phenyl]-1,3-thiazol-2-amine


Mass: 485.647 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H31N7S
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.33 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.1 M Sodium citrate, 73 mM HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.975631 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975631 Å / Relative weight: 1
ReflectionResolution: 2.1→48.53 Å / Num. obs: 17508 / % possible obs: 98 % / Redundancy: 25.797 % / Biso Wilson estimate: 57.632 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.11 / Χ2: 0.81 / Net I/σ(I): 19.65
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.2326.7421.9181.927270.751.95596.8
2.23-2.3826.1381.1513.3825800.8961.17397.4
2.38-2.5726.2890.6246.324230.9730.63697.7
2.57-2.8126.9850.37310.8622500.9910.3898
2.81-3.1425.0870.19119.8320650.9970.19598.1
3.14-3.6326.7230.10435.4718380.9980.10698.7
3.63-4.4425.3110.07247.8615780.9990.07398.9
4.44-6.2523.3210.06251.8112700.9990.06499.1
6.25-48.5321.1020.05355.367770.9990.05499.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KCG

4kcg


Resolution: 2.1→48.53 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.959 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.206 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.236 874 5 %RANDOM
Rwork0.1958 ---
obs0.1979 16597 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.41 Å2 / Biso mean: 55.748 Å2 / Biso min: 37.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å2-0 Å2-0 Å2
2--0.86 Å2-0 Å2
3----1.71 Å2
Refinement stepCycle: final / Resolution: 2.1→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1915 0 61 42 2018
Biso mean--61 50.03 -
Num. residues----229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132038
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151875
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.6632767
X-RAY DIFFRACTIONr_angle_other_deg1.3091.5854324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6445232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.85823.246114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.6615361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0071511
X-RAY DIFFRACTIONr_chiral_restr0.0750.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022266
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02486
LS refinement shellResolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 63 -
Rwork0.291 1190 -
all-1253 -
obs--96.83 %

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