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- PDB-6yt1: Mtb TMK crystal structure in complex with compound 26 -

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Basic information

Entry
Database: PDB / ID: 6yt1
TitleMtb TMK crystal structure in complex with compound 26
ComponentsThymidylate kinase
KeywordsTRANSFERASE / Kinase activity / Inhibitor complex
Function / homology
Function and homology information


TMP metabolic process / dTMP kinase / dTMP kinase activity / dUDP biosynthetic process / dTDP biosynthetic process / dTTP biosynthetic process / GTP binding / magnesium ion binding / protein homodimerization activity / ATP binding ...TMP metabolic process / dTMP kinase / dTMP kinase activity / dUDP biosynthetic process / dTDP biosynthetic process / dTTP biosynthetic process / GTP binding / magnesium ion binding / protein homodimerization activity / ATP binding / cytosol / cytoplasm
Similarity search - Function
Thymidylate kinase, conserved site / Thymidylate kinase signature. / Thymidylate kinase / Thymidylate kinase-like domain / Thymidylate kinase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
CITRIC ACID / Chem-PK5 / Thymidylate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMerceron, R. / De Munck, S. / Jian, Y. / Munier-Lehmann, H. / Van Calenbergh, S. / Savvides, S.N.
CitationJournal: Eur.J.Med.Chem. / Year: 2020
Title: Endeavors towards transformation of M. tuberculosis thymidylate kinase (MtbTMPK) inhibitors into potential antimycobacterial agents.
Authors: Jian, Y. / Merceron, R. / De Munck, S. / Forbes, H.E. / Hulpia, F. / Risseeuw, M.D.P. / Van Hecke, K. / Savvides, S.N. / Munier-Lehmann, H. / Boshoff, H.I.M. / Van Calenbergh, S.
History
DepositionApr 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)46,9607
Polymers45,3252
Non-polymers1,6355
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-5 kcal/mol
Surface area15880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.740, 87.740, 112.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-449-

HOH

21B-471-

HOH

31B-509-

HOH

41B-511-

HOH

51B-522-

HOH

61B-527-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETVALVAL(chain 'A' and (resid 1 through 18 or (resid 19...AA1 - 781 - 78
12THRTHRASPASP(chain 'A' and (resid 1 through 18 or (resid 19...AA80 - 9480 - 94
13TYRTYRVALVAL(chain 'A' and (resid 1 through 18 or (resid 19...AA96 - 9796 - 97
14ASNASNLEULEU(chain 'A' and (resid 1 through 18 or (resid 19...AA100 - 128100 - 128
15PROPROVALVAL(chain 'A' and (resid 1 through 18 or (resid 19...AA131 - 141131 - 141
16GLUGLUGLUGLU(chain 'A' and (resid 1 through 18 or (resid 19...AA166166
17ALAALAGLNGLN(chain 'A' and (resid 1 through 18 or (resid 19...AA169 - 172169 - 172
18ARGARGALAALA(chain 'A' and (resid 1 through 18 or (resid 19...AA174 - 183174 - 183
19GLYGLYPROPRO(chain 'A' and (resid 1 through 18 or (resid 19...AA186 - 210186 - 210
110PK5PK5PK5PK5(chain 'A' and (resid 1 through 18 or (resid 19...AC301
111HOHHOHHOHHOH(chain 'A' and (resid 1 through 18 or (resid 19...AH401
212METMETVALVAL(chain 'B' and (resid 1 through 13 or (resid 14...BB1 - 781 - 78
213THRTHRASPASP(chain 'B' and (resid 1 through 13 or (resid 14...BB80 - 9480 - 94
214TYRTYRVALVAL(chain 'B' and (resid 1 through 13 or (resid 14...BB96 - 9796 - 97
215ASNASNLEULEU(chain 'B' and (resid 1 through 13 or (resid 14...BB100 - 128100 - 128
216PROPROVALVAL(chain 'B' and (resid 1 through 13 or (resid 14...BB131 - 141131 - 141
217GLUGLUGLUGLU(chain 'B' and (resid 1 through 13 or (resid 14...BB148148
218ALAALAGLNGLN(chain 'B' and (resid 1 through 13 or (resid 14...BB169 - 172169 - 172
219ARGARGALAALA(chain 'B' and (resid 1 through 13 or (resid 14...BB174 - 183174 - 183
220GLYGLYPROPRO(chain 'B' and (resid 1 through 13 or (resid 14...BB186 - 210186 - 210
221PK5PK5PK5PK5(chain 'B' and (resid 1 through 13 or (resid 14...BE301
222HOHHOHHOHHOH(chain 'B' and (resid 1 through 13 or (resid 14...BI401

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Components

#1: Protein Thymidylate kinase / Thymidine monophosphate kinase / dTMP kinase / TMPK


Mass: 22662.525 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: tmk, Rv3247c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WKE1, dTMP kinase
#2: Chemical ChemComp-PK5 / 2-ethyl-~{N}-[[4-[4-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]piperidin-1-yl]phenyl]methyl]-1,2,3,5,6,7,8,8~{a}-octahydroimidazo[1,2-a]pyridine-3-carboxamide


Mass: 529.074 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H37ClN6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.39 Å3/Da / Density % sol: 48.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium tartrate dibasic, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.9→41.7 Å / Num. obs: 35305 / % possible obs: 98.85 % / Redundancy: 13.7 % / Biso Wilson estimate: 27.71 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.109 / Net I/σ(I): 22.1
Reflection shellResolution: 1.9→1.99 Å / Num. unique obs: 5324 / CC1/2: 0.95 / Rrim(I) all: 0.729

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Processing

Software
NameVersionClassification
BUSTERrefinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NRQ

5nrq


Resolution: 1.9→40.88 Å / SU ML: 0.2256 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.1596
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2033 1764 5 %
Rwork0.1673 33524 -
obs0.1691 35288 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.17 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2793 0 98 262 3153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072998
X-RAY DIFFRACTIONf_angle_d0.72894098
X-RAY DIFFRACTIONf_chiral_restr0.0461451
X-RAY DIFFRACTIONf_plane_restr0.0046581
X-RAY DIFFRACTIONf_dihedral_angle_d18.46541067
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.40971350.35342549X-RAY DIFFRACTION99.78
1.95-2.010.25991320.23132508X-RAY DIFFRACTION99.89
2.01-2.070.23161330.18412552X-RAY DIFFRACTION99.93
2.07-2.150.21331320.16612535X-RAY DIFFRACTION99.96
2.15-2.230.24181330.19452518X-RAY DIFFRACTION98.95
2.23-2.340.30691340.21412538X-RAY DIFFRACTION99.4
2.34-2.460.18311350.15282564X-RAY DIFFRACTION100
2.46-2.610.18371340.14382543X-RAY DIFFRACTION100
2.61-2.810.18941360.15272589X-RAY DIFFRACTION99.96
2.81-3.10.22361360.1522592X-RAY DIFFRACTION100
3.1-3.540.17371370.15392600X-RAY DIFFRACTION99.96
3.55-4.470.16941400.13832652X-RAY DIFFRACTION99.96
4.47-40.880.1921470.17442784X-RAY DIFFRACTION99.83
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)
19.19317190279-2.72282578672-4.364807847632.742152548081.678498557336.491135401220.0245753639782-0.7306117652420.4635753036530.2887786213260.219206790639-0.202929343202-0.1926653026230.595393369594-0.2376828968550.394562251403-0.03065998796440.05719968025550.251229210317-0.01178033141590.29649546340293.277055916543.1275010065134.593360013
27.59438377707-4.21895365426-3.819440089133.274733660723.429036190564.096186713460.0170439625738-0.5919763926170.4051456447180.2706694890780.172640249889-0.353769861883-0.2398052573820.063640510825-0.1598398340390.3224373135340.002258454459570.06384567105870.283823548934-0.03625858224170.16617136007288.266427126334.0786353687136.727042661
34.37017416978-3.6514307748-2.638445096894.241207617692.141748685762.69016319832-0.030358200216-0.127892226171-0.199400374790.214292230665-0.03368607810930.1718704350380.00596579792744-0.03864394142410.1437223802730.228185038125-0.06157835510560.02789430143470.2074770107190.01350083089740.18867876252293.932337688323.4218800852129.350541173
44.17666390654-4.16853503882-6.022825078764.667002719595.864776105798.699514358030.146774581672-0.05337354137980.167841592051-0.01200052267710.00632357226483-0.110794636724-0.237802655550.0326412552871-0.4577266583550.250548861816-0.02890328399950.0289190231070.1795450405410.03842756567490.21053664765594.062109387634.4780604095127.77560825
53.845122669364.70323502583-4.529756945898.30658759193-3.182945977257.65405020273-0.2399060583610.4807598039120.153618976233-0.357255536680.345702342550.1339423910760.01609738945080.0117601879782-0.1348998379230.219132896438-0.01889257596620.03404035070780.236275953239-0.02389314988750.17232303829797.555616805629.1221274556114.756278374
65.5644791017-1.57163354829-1.242518519.050239391891.59662279744.27544969223-0.0364950133720.0515612707646-0.569956569963-0.101964441841-0.1012247597051.02431202933-0.188485175796-0.4060435020750.03332254747680.204791154691-0.004316026228080.02963517442360.3292519444130.008973977608960.29454670283484.993638995331.3803053453121.279613218
74.94695902043-1.4250333914-0.3507726265764.93438527696-0.2804660642982.135446542420.0151832639382-0.1943320135850.2825968918340.43843791712-0.00484067489279-0.438841903228-0.1805121807890.311968904577-0.05550591222440.294489966508-0.07732299450960.02169259355170.2145731342040.009792394894680.247165817956101.83220214139.4529696085124.533545341
87.55754586322-6.08415497277-4.54342807156.546374027245.300035750626.426395409080.672242489789-0.5490358590610.939441725785-0.172540236579-0.3564194950230.749146546845-0.488606840422-0.643760202921-0.3467532355560.7001353707220.04547896671170.1954439263730.332992938315-0.03041512153950.64406506899887.682322448453.0932607285130.97290183
96.130203495931.84006520541-4.348484836572.99928748525-0.5356122402756.11445061148-0.2441016599610.321425275528-0.183139635158-0.0677316592160.2101441378270.242677823730.584863588314-0.632537292946-0.06815983608070.307603715044-0.0631839200181-0.01695635671950.2751012766940.06187608728360.22738805005583.0145410058-8.52139234667123.795304533
105.808493707123.7847835471-2.304318933374.00797428798-2.538675582414.18885262623-0.0407171581116-0.04015057700350.0155414754428-0.1881001941730.09037053415090.1440483186490.226789309137-0.312826298282-0.02367759735350.1968221999440.02219459119490.00622740213710.221816267141-0.02074802272120.14781182962187.42038405718.11318711959120.684296282
112.546697311181.14049445255-0.6156862957342.40859645302-0.8107721292873.062367382710.159042764632-0.20942873655-0.0332382390010.239826290822-0.123626013910.03726251039960.0278113397362-0.0880699105152-0.0276106270560.238846538541-0.0017753208373-0.007039662582160.2542305473830.02993906214750.14742674842192.01477068083.90265599292129.470443572
122.78302013720.540786779159-1.587472037533.829758059731.055637612014.03363189010.1737794789580.123351261984-0.224931520945-0.199537967895-0.182848988602-0.3668278327050.192509131807-0.0142371958195-0.01671070675950.2985037879290.086647220492-0.03783633709640.2961099498160.1012289134940.26191931631796.1138615091-4.57176424486124.571932806
134.568309298642.19503885216-2.298051932223.76645823723-1.085968908494.51355764041-0.0375504859354-0.219302276122-0.280117184406-0.00135285393701-0.0753904229758-0.1520413283790.7284185605710.2860362242340.1411306398560.3543072435930.0829254180768-0.02199797771560.2352512554530.0554290760290.29083170408997.2276993214-9.08789973686126.772574216
143.51924580653-2.287262817653.715667705625.78045030492-3.185629820524.05690886850.0287314602443-0.559710227983-1.287286298180.8490917276130.1666339236561.050393462431.40592797797-1.09555017803-0.00582002703380.670457753543-0.1871287980040.0689007782690.3832779890550.08422425326880.48111383428181.1137218466-17.9023306834131.800933725
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 42 )
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 87 )
4X-RAY DIFFRACTION4chain 'A' and (resid 88 through 107 )
5X-RAY DIFFRACTION5chain 'A' and (resid 108 through 124 )
6X-RAY DIFFRACTION6chain 'A' and (resid 125 through 134 )
7X-RAY DIFFRACTION7chain 'A' and (resid 135 through 199 )
8X-RAY DIFFRACTION8chain 'A' and (resid 200 through 210 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 26 )
10X-RAY DIFFRACTION10chain 'B' and (resid 27 through 62 )
11X-RAY DIFFRACTION11chain 'B' and (resid 63 through 124 )
12X-RAY DIFFRACTION12chain 'B' and (resid 125 through 170 )
13X-RAY DIFFRACTION13chain 'B' and (resid 171 through 199 )
14X-RAY DIFFRACTION14chain 'B' and (resid 200 through 210 )

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