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- PDB-5nr7: Mtb TMK crystal structure in complex with compound 43 -

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Basic information

Entry
Database: PDB / ID: 5nr7
TitleMtb TMK crystal structure in complex with compound 43
ComponentsThymidylate kinase
KeywordsTRANSFERASE / Thymidylate kinase / Nucleotide Binding / inhibitor
Function / homology
Function and homology information


TMP metabolic process / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / GTP binding / magnesium ion binding / protein homodimerization activity / ATP binding ...TMP metabolic process / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-YUI / Thymidylate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMerceron, R. / Song, L. / Munier-Lehmann, H. / Van Calenbergh, S. / Savvides, S.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Structure Guided Lead Generation toward Nonchiral M. tuberculosis Thymidylate Kinase Inhibitors.
Authors: Song, L. / Merceron, R. / Gracia, B. / Quintana, A.L. / Risseeuw, M.D.P. / Hulpia, F. / Cos, P. / Ainsa, J.A. / Munier-Lehmann, H. / Savvides, S.N. / Van Calenbergh, S.
History
DepositionApr 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)46,3506
Polymers45,3252
Non-polymers1,0254
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-28 kcal/mol
Surface area15150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.630, 73.630, 72.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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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 (strain ATCC 25618 / H37Rv) (bacteria)
Gene: tmk, Rv3247c / Production host: Escherichia coli (E. coli) / Strain (production host): BLi5 / References: UniProt: P9WKE1, dTMP kinase
#2: Chemical ChemComp-YUI / 1-[1-[[4-(3-chloranylphenoxy)quinolin-2-yl]methyl]piperidin-4-yl]-5-methyl-pyrimidine-2,4-dione


Mass: 476.955 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H25ClN4O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.52 Å3/Da / Density % sol: 51.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5, 4.3 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 18395 / % possible obs: 100 % / Redundancy: 8.46 % / Biso Wilson estimate: 50.075 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.0153 / Rsym value: 0.0144 / Net I/σ(I): 11.11
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 8.41 % / Mean I/σ(I) obs: 1.63 / Num. unique obs: 1359 / CC1/2: 0.375 / Rrim(I) all: 1.267 / Rsym value: 1.188 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UNR

4unr


Resolution: 2.35→47.984 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 24.99
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 920 5 %Random selection
Rwork0.1923 ---
obs0.194 18394 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.35→47.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2668 0 70 97 2835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022792
X-RAY DIFFRACTIONf_angle_d0.4743810
X-RAY DIFFRACTIONf_dihedral_angle_d13.6211636
X-RAY DIFFRACTIONf_chiral_restr0.035432
X-RAY DIFFRACTIONf_plane_restr0.002548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.47390.33181310.29022489X-RAY DIFFRACTION100
2.4739-2.62890.30351320.27722509X-RAY DIFFRACTION100
2.6289-2.83190.26551310.25372499X-RAY DIFFRACTION100
2.8319-3.11680.29911310.242482X-RAY DIFFRACTION100
3.1168-3.56770.24631320.19492509X-RAY DIFFRACTION100
3.5677-4.49440.18681310.15142481X-RAY DIFFRACTION100
4.4944-47.99410.17711320.15812505X-RAY DIFFRACTION100
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)
14.1928-0.50011.45163.57811.61843.1427-0.07780.10990.59990.05180.0718-0.5203-0.02260.0828-0.01420.2611-0.0123-0.02070.32160.04850.3896-2.528720.3687-13.4767
26.29173.7462.88883.76471.85083.8314-0.42530.08810.7543-0.08430.07420.2614-0.17310.00780.24630.3745-0.0115-0.04230.3415-0.09130.38719.803829.110313.6707
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 209)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 208)

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