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- PDB-5mql: Crystal structure of dCK mutant C3S in complex with masitinib and UDP -

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Basic information

Entry
Database: PDB / ID: 5mql
TitleCrystal structure of dCK mutant C3S in complex with masitinib and UDP
ComponentsDeoxycytidine kinase
KeywordsTRANSFERASE / Deoxycytidine kinase / dCK / masitinib
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 / phosphorylation / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / Masitinib / URIDINE-5'-DIPHOSPHATE / Deoxycytidine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsRebuffet, E. / Hammam, K. / Saez-Ayala, M. / Gros, L. / Lopez, S. / Hajem, B. / Humbert, M. / Baudelet, E. / Audebert, S. / Betzi, S. ...Rebuffet, E. / Hammam, K. / Saez-Ayala, M. / Gros, L. / Lopez, S. / Hajem, B. / Humbert, M. / Baudelet, E. / Audebert, S. / Betzi, S. / Lugari, A. / Combes, S. / Pez, D. / Letard, S. / Mansfield, C. / Moussy, A. / de Sepulveda, P. / Morelli, X. / Dubreuil, P.
Funding support France, 1items
OrganizationGrant numberCountry
ARCSL220130606659 France
CitationJournal: Nat Commun / Year: 2017
Title: Dual protein kinase and nucleoside kinase modulators for rationally designed polypharmacology.
Authors: Hammam, K. / Saez-Ayala, M. / Rebuffet, E. / Gros, L. / Lopez, S. / Hajem, B. / Humbert, M. / Baudelet, E. / Audebert, S. / Betzi, S. / Lugari, A. / Combes, S. / Letard, S. / Casteran, N. / ...Authors: Hammam, K. / Saez-Ayala, M. / Rebuffet, E. / Gros, L. / Lopez, S. / Hajem, B. / Humbert, M. / Baudelet, E. / Audebert, S. / Betzi, S. / Lugari, A. / Combes, S. / Letard, S. / Casteran, N. / Mansfield, C. / Moussy, A. / De Sepulveda, P. / Morelli, X. / Dubreuil, P.
History
DepositionDec 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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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
C: Deoxycytidine kinase
D: Deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,84712
Polymers136,0934
Non-polymers2,7548
Water32418
1
A: Deoxycytidine kinase
B: Deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6616
Polymers68,0462
Non-polymers1,6144
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-33 kcal/mol
Surface area18800 Å2
MethodPISA
2
C: Deoxycytidine kinase
D: Deoxycytidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1866
Polymers68,0462
Non-polymers1,1404
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-49 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.330, 88.330, 342.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Deoxycytidine kinase / / dCK


Mass: 34023.195 Da / Num. of mol.: 4 / Mutation: C9S,C45S,C59S
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

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Non-polymers , 5 types, 26 molecules

#2: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-G65 / Masitinib / Masitinib


Mass: 498.642 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H30N6OS / Comment: inhibitor*YM
#4: Chemical ChemComp-DCM / 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / Deoxycytidine monophosphate


Mass: 307.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O7P
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.45 Å3/Da / Density % sol: 49.87 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM sodium acetate, 20% PEG 3350, 50 mM NaCl, 24h soaking with 10 mM Masitinib

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.885602 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885602 Å / Relative weight: 1
ReflectionResolution: 3.25→42.8 Å / Num. obs: 22378 / % possible obs: 100 % / Redundancy: 8.2 % / Biso Wilson estimate: 138.18 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.2677 / Net I/σ(I): 11.94
Reflection shellResolution: 3.25→3.366 Å / Redundancy: 8.6 % / Num. unique obs: 2164 / CC1/2: 0.832 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P60

1p60


Resolution: 3.25→47.8 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.858 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.519
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1120 5 %RANDOM
Rwork0.215 ---
obs0.219 22381 99.9 %-
Displacement parametersBiso mean: 97.83 Å2
Baniso -1Baniso -2Baniso -3
1--18.3324 Å20 Å20 Å2
2---18.3324 Å20 Å2
3---36.6649 Å2
Refine analyzeLuzzati coordinate error obs: 0.47 Å
Refinement stepCycle: 1 / Resolution: 3.25→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7332 0 177 18 7527
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0117702HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1610509HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2587SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes196HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1138HARMONIC5
X-RAY DIFFRACTIONt_it7702HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.69
X-RAY DIFFRACTIONt_other_torsion22.31
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion998SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9078SEMIHARMONIC4
LS refinement shellResolution: 3.25→3.41 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.3249 146 5 %
Rwork0.2887 2773 -
all0.2905 2919 -
obs--99.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.1785-0.3250.88062.9868-0.92532.70250.0119-0.04-0.05260.1910.076-0.10960.1774-0.3633-0.0879-0.086-0.1366-0.0577-0.1270.045-0.14329.905768.59497.3041
22.93050.39640.3131.60420.53462.33340.03280.1071-0.2805-0.07780.02490.07350.29120.2422-0.0577-0.02320.053-0.0686-0.27490.01210.040464.906768.811521.0617
33.6920.17930.36683.70490.11143.0413-0.00020.2761-0.24090.02980.1660.0822-0.0380.5071-0.1657-0.21020.0431-0.018-0.16960.0602-0.060425.523444.66634.2287
43.4217-0.31941.57143.8967-0.57513.9284-0.10730.25180.09580.140.0637-0.35390.2761-0.22830.0436-0.1727-0.0901-0.0604-0.23790.1076-0.0722-1.728421.831323.9017
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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