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- PDB-4qgh: S.aureus TMK in complex with potent inhibitor compound 47 -

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Basic information

Entry
Database: PDB / ID: 4qgh
TitleS.aureus TMK in complex with potent inhibitor compound 47
ComponentsThymidylate kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / thymidine monphosphate / soluble / TRANSFERASE-TRANSFERASE INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / ATP binding
Similarity search - Function
Thymidylate kinase, conserved site / Thymidylate kinase signature. / Thymidylate kinase / Thymidylate kinase-like domain / Thymidylate 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-32E / Thymidylate kinase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsOlivier, N.B.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Antibacterial inhibitors of gram-positive thymidylate kinase: structure-activity relationships and chiral preference of a new hydrophobic binding region.
Authors: Kawatkar, S.P. / Keating, T.A. / Olivier, N.B. / Breen, J.N. / Green, O.M. / Guler, S.Y. / Hentemann, M.F. / Loch, J.T. / McKenzie, A.R. / Newman, J.V. / Otterson, L.G. / Martinez-Botella, G.
History
DepositionMay 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: 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 / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _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: Thymidylate kinase
B: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9974
Polymers46,9092
Non-polymers1,0882
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-19 kcal/mol
Surface area17900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.639, 90.140, 50.455
Angle α, β, γ (deg.)90.00, 99.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thymidylate kinase / dTMP kinase


Mass: 23454.586 Da / Num. of mol.: 2 / Fragment: TMK / Mutation: none
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: N315 / Gene: SAR0483, tmk / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q6GJI9, dTMP kinase
#2: Chemical ChemComp-32E / 2-(3-chlorophenoxy)-3-fluoro-4-{(1S)-3-methyl-1-[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl]butyl}benzoic acid


Mass: 544.014 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H31ClFN3O5
#3: 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: 2.18 Å3/Da / Density % sol: 43.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: To obtain the inhibitor bound crystal form of TMK-S.aureus crystals were initially grown in the absence of compound using the sitting drop method at 293 K with a reservoir solution of 100 mM ...Details: To obtain the inhibitor bound crystal form of TMK-S.aureus crystals were initially grown in the absence of compound using the sitting drop method at 293 K with a reservoir solution of 100 mM PCPT (propionate-cacodylate-bistris propane buffer) pH 7-8, 21-24% PEG 3350, 200 mM Mg2Cl using 1:1 protein:reservoir solution with the protein solution at 13 mg/mL. Crystals were harvested and soaked overnight in a solution containing 100 mM PCPT, 35% PEG 3350, 200 mM Mg2Cl and 1-2 mM or compound from a 100 mM DMSO stock. After soaking the crystals were cryoprotected by soaking for 15 minutes in compound-soak solution supplemented with 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP
PH range: 7-8

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.978 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 30, 2011 / Details: monochrom. diamond (111)
RadiationMonochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.781→29.297 Å / Num. all: 37864 / Num. obs: 37864 / % possible obs: 98.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 20.8 Å2 / Rsym value: 0.036 / Net I/σ(I): 20.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.78-1.883.40.1684.60.168196.7
1.88-1.993.50.1156.70.115198.5
1.99-2.133.60.0829.30.082198.7
2.13-2.33.60.06411.20.064198.9
2.3-2.523.60.05213.10.052199.1
2.52-2.823.60.042160.042199.4
2.82-3.253.60.03319.20.033199.6
3.25-3.983.60.02425.80.024199.4
3.98-5.633.60.02310.02199
5.63-29.2973.50.02125.80.021192.7

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
BUSTER-TNTBUSTER 2.11.5refinement
PDB_EXTRACT3.14data extraction
JDirectordata collection
PROCESSdata reduction
AMoREphasing
BUSTER2.11.5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→28.36 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.9195 / SU R Cruickshank DPI: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2074 1891 5 %RANDOM
Rwork0.1763 ---
obs0.1779 37830 98.08 %-
all-38570 --
Displacement parametersBiso mean: 24.03 Å2
Baniso -1Baniso -2Baniso -3
1--2.9782 Å20 Å2-5.4041 Å2
2--5.7482 Å20 Å2
3----2.77 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.78→28.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3096 0 76 267 3439
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013247HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.034403HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1149SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes86HARMONIC2
X-RAY DIFFRACTIONt_gen_planes488HARMONIC5
X-RAY DIFFRACTIONt_it3247HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.3
X-RAY DIFFRACTIONt_other_torsion16.19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion433SEMIHARMONIC5
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_contact4024SEMIHARMONIC4
LS refinement shellResolution: 1.78→1.83 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2143 123 4.43 %
Rwork0.1784 2652 -
all0.1801 2775 -
obs--98.08 %

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