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- PDB-4unq: Mtb TMK in complex with compound 36 -

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Basic information

Entry
Database: PDB / ID: 4unq
TitleMtb TMK in complex with compound 36
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 / 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-H6D / : / Thymidylate kinase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / 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 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
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_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)45,2365
Polymers44,5282
Non-polymers7083
Water3,117173
1
A: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6062
Polymers22,2641
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6293
Polymers22,2641
Non-polymers3652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.459, 75.459, 71.579
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: 22264.113 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: F2GKC3, UniProt: P9WKE1*PLUS, dTMP kinase
#2: Chemical ChemComp-H6D / 4-[(R)-methylsulfinyl]-2-oxo-6-[3-(trifluoromethoxy)phenyl]-1,2-dihydropyridine-3-carbonitrile


Mass: 342.293 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H9F3N2O3S
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.64 Å3/Da / Density % sol: 53.85 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU CCD / Detector: CCD / Date: Oct 10, 2009 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.846
11-H-K, K, -L20.154
ReflectionResolution: 2.3→65.4 Å / Num. obs: 20011 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.5 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G3U

1g3u


Resolution: 2.3→65.36 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 12.459 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21289 987 4.9 %RANDOM
Rwork0.17469 ---
obs0.17648 18996 98.54 %-
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: 41.485 Å2
Baniso -1Baniso -2Baniso -3
1-6.72 Å20 Å20 Å2
2--6.72 Å20 Å2
3----13.44 Å2
Refinement stepCycle: LAST / Resolution: 2.3→65.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2736 0 47 173 2956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212854
X-RAY DIFFRACTIONr_bond_other_d0.0010.021827
X-RAY DIFFRACTIONr_angle_refined_deg1.3471.9433890
X-RAY DIFFRACTIONr_angle_other_deg0.90234410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3355374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.98222.456114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.47515403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0031525
X-RAY DIFFRACTIONr_chiral_restr0.0720.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023338
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02631
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_it0.7121.51852
X-RAY DIFFRACTIONr_mcbond_other0.1531.5778
X-RAY DIFFRACTIONr_mcangle_it1.30722891
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1431002
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4784.5999
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: 2.299→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 60 -
Rwork0.241 1400 -
obs--96.56 %
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)
11.6477-0.17480.13442.1592-0.81752.1274-0.0346-0.0479-0.0870.0041-0.0437-0.0252-0.0272-0.00590.07830.02890.00940.03640.04140.00910.136118.53737.0049-13.4882
20.9946-0.5855-0.02163.7452-2.22252.68010.10440.0754-0.0475-0.24070.07030.1870.226-0.1661-0.17470.0471-0.0145-0.06030.04820.05660.170518.147913.311213.7866
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 209
2X-RAY DIFFRACTION2B1 - 209

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