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- PDB-5nq5: Mtb TMK crystal structure in complex with compound 1 -

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Basic information

Entry
Database: PDB / ID: 5nq5
TitleMtb TMK crystal structure in complex with compound 1
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 / phosphorylation / GTP binding / magnesium ion binding / protein homodimerization activity ...TMP metabolic process / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / phosphorylation / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-952 / Thymidylate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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 19, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0542
Polymers22,6631
Non-polymers3911
Water0
1
A: Thymidylate kinase
hetero molecules

A: Thymidylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1084
Polymers45,3252
Non-polymers7832
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area1630 Å2
ΔGint-8 kcal/mol
Surface area16360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.390, 71.390, 133.750
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: 22662.525 Da / Num. of mol.: 1
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) / Variant (production host): BLi5 / References: UniProt: P9WKE1, dTMP kinase
#2: Chemical ChemComp-952 / 5-methyl-1-[(3~{S})-1-[(3-phenoxyphenyl)methyl]piperidin-3-yl]pyrimidine-2,4-dione


Mass: 391.463 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H25N3O3

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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: 4.34 Å3/Da / Density % sol: 71.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 10 % PEG 6000, 5 % MPD / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 9634 / % possible obs: 99.5 % / Redundancy: 7.36 % / CC1/2: 0.999 / Rrim(I) all: 0.063 / Rsym value: 0.058 / Net I/σ(I): 16.97
Reflection shellResolution: 2.85→2.92 Å / Redundancy: 7.73 % / Mean I/σ(I) obs: 1.59 / Num. unique obs: 681 / CC1/2: 0.725 / Rrim(I) all: 1.276 / Rsym value: 1.191 / % possible all: 99.6

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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: 4UNP

4unp


Resolution: 2.85→44.583 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 32.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2393 482 5.01 %Random selection
Rwork0.2008 ---
obs0.2027 9629 99.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→44.583 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1373 0 29 0 1402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011443
X-RAY DIFFRACTIONf_angle_d0.3021969
X-RAY DIFFRACTIONf_dihedral_angle_d10.797848
X-RAY DIFFRACTIONf_chiral_restr0.033222
X-RAY DIFFRACTIONf_plane_restr0.002276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8501-3.26250.31131570.28312978X-RAY DIFFRACTION99
3.2625-4.10990.25941580.23423006X-RAY DIFFRACTION100
4.1099-44.58880.22331670.17823163X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -26.6471 Å / Origin y: 24.2293 Å / Origin z: -7.8962 Å
111213212223313233
T0.7256 Å2-0.165 Å20.0943 Å2-0.858 Å2-0.115 Å2--0.6886 Å2
L3.2767 °21.3384 °2-1.2978 °2-7.9555 °2-4.4843 °2--8.1992 °2
S0.0342 Å °-0.0247 Å °-0.0116 Å °0.424 Å °0.0038 Å °0.6049 Å °-0.032 Å °-0.3601 Å °-0.0627 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 1 through 212)

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