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- PDB-4unr: Mtb TMK in complex with compound 23 -

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Basic information

Entry
Database: PDB / ID: 4unr
TitleMtb TMK in complex with compound 23
ComponentsThymidylate kinase
KeywordsTRANSFERASE / ATP TMP PHOSPHOTRANSFERASE
Function / homology
Function and homology information


TMP metabolic process / dTMP kinase / dUDP biosynthetic process / dTDP biosynthetic process / dTMP kinase activity / dTTP biosynthetic process / GTP binding / magnesium ion binding / protein homodimerization activity / ATP binding ...TMP metabolic process / dTMP kinase / dUDP biosynthetic process / dTDP biosynthetic process / dTMP kinase activity / dTTP biosynthetic process / GTP binding / magnesium ion binding / protein homodimerization activity / ATP binding / cytoplasm / cytosol
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-QZE / Thymidylate kinase / Thymidylate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 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 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Sep 25, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / exptl_crystal_grow / pdbx_database_status / reflns / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.4Jan 10, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _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)45,3946
Polymers44,5282
Non-polymers8654
Water4,720262
1
A: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6973
Polymers22,2641
Non-polymers4332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6973
Polymers22,2641
Non-polymers4332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.508, 75.508, 71.447
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 / dTMP kinase


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)
Gene: tmk, tmk_1, tmk_2, DKC2_3451, DSI35_30710, ERS007657_00125, ERS007661_00085, ERS007679_02297, ERS007681_01491, ERS007703_02607, ERS007741_01144, ERS023446_00222, ERS024213_00798, ERS027644_ ...Gene: tmk, tmk_1, tmk_2, DKC2_3451, DSI35_30710, ERS007657_00125, ERS007661_00085, ERS007679_02297, ERS007681_01491, ERS007703_02607, ERS007741_01144, ERS023446_00222, ERS024213_00798, ERS027644_01165, ERS027646_01076, ERS027651_00812, ERS027652_02895, ERS027653_00561, ERS027654_03560, ERS027656_02366, ERS027659_02658, ERS027666_03206, ERS031537_04492, ERS124361_01566, EU767_17775, EU768_12605, EU769_05785, EU770_08300, EU771_12795, EU773_12630, EU774_05685, EU775_05915, EU776_12880, EU777_03925, EUB02_06795, EUB03_06915, EUB06_16595, EUB07_02595, EUB08_14260, EUB09_06965, EUB10_01690, EUB11_02810, EUB12_02780, EUB13_09520, EUB14_09750, EUB16_09100, SAMEA2682835_07050, SAMEA2683035_03767
Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: A0A045HB39, UniProt: P9WKE1*PLUS, dTMP kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-QZE / 4-[3-cyano-2-oxo-7-(1H-pyrazol-4-yl)-5,6-dihydro-1H-benzo[h]quinolin-4-yl]benzoic acid


Mass: 408.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H16N4O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 53.42 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / Details: Well soln: 0.1M PCTP, pH6.8, 4.5M NaCl

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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: Mar 31, 2010 / 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
ReflectionResolution: 1.98→71 Å / Num. obs: 31560 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.3
Reflection shellResolution: 1.98→2.1 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.3 / % possible all: 95.3

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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: 1.98→65.39 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.18 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20759 1591 5.1 %RANDOM
Rwork0.17817 ---
obs0.17968 29826 99.04 %-
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: 29.771 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20.2 Å20 Å2
2--0.41 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.98→65.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2722 0 64 262 3048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212862
X-RAY DIFFRACTIONr_bond_other_d0.0030.021827
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.9713904
X-RAY DIFFRACTIONr_angle_other_deg0.90934412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8665374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.50222.613111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91215398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9291523
X-RAY DIFFRACTIONr_chiral_restr0.0680.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023398
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02635
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_it0.731.51852
X-RAY DIFFRACTIONr_mcbond_other0.1491.5778
X-RAY DIFFRACTIONr_mcangle_it1.34322889
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.99431010
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2744.51015
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: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 116 -
Rwork0.245 2045 -
obs--92.63 %
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)
10.98560.11190.26790.82760.38510.93370.00260.0352-0.064-0.0022-0.0037-0.0056-0.01170.04040.00120.0116-0.00830.00790.0124-0.0080.010857.009237.000713.4287
20.2903-0.0774-0.31321.81391.37121.43870.0544-0.0463-0.00960.1210.0805-0.17910.09370.0715-0.1350.04410.0023-0.03770.0414-0.03670.061957.394213.2788-13.7597
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 209
2X-RAY DIFFRACTION2B1 - 209

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