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- PDB-4unp: Mtb TMK in complex with compound 34 -

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Basic information

Entry
Database: PDB / ID: 4unp
TitleMtb TMK in complex with compound 34
ComponentsTHYMIDYLATE KINASE
KeywordsTRANSFERASE / TRANSFER (ATP TMP PHOSPHOTRANSFERASE) / KINASE
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 / metal ion 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
5-methyl-7-propyl-1,6-naphthyridin-2(1H)-one / Thymidylate kinase / Thymidylate kinase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRead, J.A. / Hussein, S. / Gingell, H. / Tucker, J.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Structure Guided Lead Generation for M. Tuberculosis Thymidylate Kinase (Mtb Tmk): Discovery of 3-Cyanopyridone and 1,6-Naphthyridin-2-One as Potent Inhibitors.
Authors: Naik, M. / Raichurkar, A. / Bandodkar, B.S. / Varun, B.V. / Bhat, S. / Kalkhambkar, R. / Murugan, K. / Menon, R. / Bhat, J. / Paul, B. / Iyer, H. / Hussein, S. / Tucker, J.A. / Vogtherr, M. ...Authors: Naik, M. / Raichurkar, A. / Bandodkar, B.S. / Varun, B.V. / Bhat, S. / Kalkhambkar, R. / Murugan, K. / Menon, R. / Bhat, J. / Paul, B. / Iyer, H. / Hussein, S. / Tucker, J.A. / Vogtherr, M. / Embrey, K.J. / Mcmiken, H. / Prasad, S. / Gill, A. / Ugarkar, B.G. / Venkatraman, J. / Read, J. / Panda, M.
History
DepositionMay 30, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4662
Polymers22,2641
Non-polymers2021
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.140, 65.140, 134.818
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein THYMIDYLATE KINASE / THYMIDINE MONOPHOSPHATE KINASE / DTMP KINASE / TMPK


Mass: 22264.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P9WKE0, UniProt: P9WKE1*PLUS, dTMP kinase
#2: Chemical ChemComp-TXW / 5-methyl-7-propyl-1,6-naphthyridin-2(1H)-one


Mass: 202.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14N2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.71 Å3/Da / Density % sol: 66.83 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: May 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→52 Å / Num. obs: 15212 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.6 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0090refinement
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G3U

1g3u


Resolution: 2.3→35.15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.957 / SU B: 12.25 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21413 746 4.9 %RANDOM
Rwork0.18667 ---
obs0.18797 14437 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.155 Å2
Baniso -1Baniso -2Baniso -3
1-3.33 Å21.67 Å20 Å2
2--3.33 Å20 Å2
3----5 Å2
Refinement stepCycle: LAST / Resolution: 2.3→35.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1347 0 15 47 1409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211430
X-RAY DIFFRACTIONr_bond_other_d0.0010.02934
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.9351952
X-RAY DIFFRACTIONr_angle_other_deg0.94532252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7945189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09322.03459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.87515204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.4761514
X-RAY DIFFRACTIONr_chiral_restr0.0840.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021686
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02319
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8121.5925
X-RAY DIFFRACTIONr_mcbond_other0.1651.5386
X-RAY DIFFRACTIONr_mcangle_it1.57821453
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4993505
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1934.5499
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 64 -
Rwork0.308 997 -
obs--96.72 %
Refinement TLS params.Method: refined / Origin x: 41.4821 Å / Origin y: 23.4226 Å / Origin z: 60.7228 Å
111213212223313233
T0.044 Å2-0.0069 Å20.0501 Å2-0.0764 Å2-0.0292 Å2--0.0789 Å2
L0.5584 °20.2656 °2-0.1184 °2-2.7688 °2-2.1745 °2--3.5132 °2
S-0.0524 Å °-0.1101 Å °-0.0004 Å °0.1555 Å °0.0431 Å °0.0862 Å °-0.0979 Å °-0.2093 Å °0.0093 Å °

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