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- PDB-6c9v: Mycobacterium tuberculosis adenosine kinase bound to (2R,3S,4R,5R... -

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Basic information

Entry
Database: PDB / ID: 6c9v
TitleMycobacterium tuberculosis adenosine kinase bound to (2R,3S,4R,5R)-2-(hydroxymethyl)-5-(6-(4-phenylpiperazin-1-yl)-9H-purin-9-yl)tetrahydrofuran-3,4-diol
ComponentsAdenosine kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Nucleoside analog / Complex / Inhibitor / Structural Genomics / PSI-2 / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


adenosine kinase / adenosine kinase activity / dGTP binding / AMP salvage / purine ribonucleoside salvage / GTP binding / magnesium ion binding / ATP binding / plasma membrane
Similarity search - Function
: / pfkB family of carbohydrate kinases signature 1. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-ERS / Adenosine kinase / Adenosine kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCrespo, R.A. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 3items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1024055 United States
Welch FoundationA-0015 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01A1095208 United States
CitationJournal: J.Med.Chem. / Year: 2019
Title: Structure-Guided Drug Design of 6-Substituted Adenosine Analogues as Potent Inhibitors of Mycobacterium tuberculosis Adenosine Kinase.
Authors: Crespo, R.A. / Dang, Q. / Zhou, N.E. / Guthrie, L.M. / Snavely, T.C. / Dong, W. / Loesch, K.A. / Suzuki, T. / You, L. / Wang, W. / O'Malley, T. / Parish, T. / Olsen, D.B. / Sacchettini, J.C.
History
DepositionJan 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: 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

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Assembly

Deposited unit
A: Adenosine kinase
B: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1639
Polymers69,0082
Non-polymers1,1557
Water10,251569
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Sedimentation coefficient
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-65 kcal/mol
Surface area23830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.084, 50.084, 264.752
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Adenosine kinase / AK


Mass: 34503.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: adoK, cbhK, MRA_2218 / Production host: Escherichia coli (E. coli)
References: UniProt: A5U4N0, UniProt: P9WID5*PLUS, adenosine kinase

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Non-polymers , 5 types, 576 molecules

#2: Chemical ChemComp-ERS / (2R,3S,4R,5R)-2-(hydroxymethyl)-5-[6-(4-phenylpiperazin-1-yl)-9H-purin-9-yl]tetrahydrofuran-3,4-diol


Mass: 412.442 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N6O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 569 / 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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 100 mM HEPES, pH 7.5, 2 M ammonium sulfate, 2% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 25, 2017
RadiationMonochromator: double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.701→43.56 Å / Num. obs: 70903 / % possible obs: 99.9 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.09756 / Net I/σ(I): 11.01
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.5145 / Mean I/σ(I) obs: 2.22 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PKM

2pkm


Resolution: 1.7→43.56 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.32
RfactorNum. reflection% reflection
Rfree0.203 3626 5.12 %
Rwork0.169 --
obs0.171 70889 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→43.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4694 0 78 569 5341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094859
X-RAY DIFFRACTIONf_angle_d1.086611
X-RAY DIFFRACTIONf_dihedral_angle_d16.2942814
X-RAY DIFFRACTIONf_chiral_restr0.059762
X-RAY DIFFRACTIONf_plane_restr0.007852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7012-1.72360.32771530.26212594X-RAY DIFFRACTION97
1.7236-1.74720.28851380.24162488X-RAY DIFFRACTION100
1.7472-1.77220.28751570.22662585X-RAY DIFFRACTION100
1.7722-1.79860.25921430.21812588X-RAY DIFFRACTION100
1.7986-1.82670.25511350.20992579X-RAY DIFFRACTION100
1.8267-1.85670.25171490.18872615X-RAY DIFFRACTION100
1.8567-1.88870.221210.18422542X-RAY DIFFRACTION100
1.8887-1.9230.20471430.17882615X-RAY DIFFRACTION100
1.923-1.960.20541420.17442595X-RAY DIFFRACTION100
1.96-20.23181350.17532613X-RAY DIFFRACTION100
2-2.04350.22051090.17152580X-RAY DIFFRACTION100
2.0435-2.09110.2071170.18182641X-RAY DIFFRACTION100
2.0911-2.14340.18851340.16952575X-RAY DIFFRACTION100
2.1434-2.20130.22361380.16352584X-RAY DIFFRACTION100
2.2013-2.26610.2111210.17042625X-RAY DIFFRACTION100
2.2661-2.33920.20121410.17532549X-RAY DIFFRACTION100
2.3392-2.42280.20111310.16342590X-RAY DIFFRACTION100
2.4228-2.51980.18231460.16562613X-RAY DIFFRACTION100
2.5198-2.63450.21561420.16042603X-RAY DIFFRACTION100
2.6345-2.77340.19361340.16282575X-RAY DIFFRACTION100
2.7734-2.94710.21471410.16392637X-RAY DIFFRACTION100
2.9471-3.17460.21221350.17792556X-RAY DIFFRACTION100
3.1746-3.4940.21451320.17392589X-RAY DIFFRACTION100
3.494-3.99930.20361650.15232576X-RAY DIFFRACTION100
3.9993-5.03780.15071750.13382578X-RAY DIFFRACTION100
5.0378-46.86110.19771490.18322578X-RAY DIFFRACTION100

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