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- PDB-6c9s: Mycobacterium tuberculosis adenosine kinase bound to (2R,3R,4S,5R... -

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Basic information

Entry
Database: PDB / ID: 6c9s
TitleMycobacterium tuberculosis adenosine kinase bound to (2R,3R,4S,5R)-2-(6-([1,1'-biphenyl]-4-ylethynyl)-9H-purin-9-yl)-5-(hydroxymethyl)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-ERP / Adenosine kinase / Adenosine kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 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)70,1038
Polymers69,0082
Non-polymers1,0956
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Sedimentation coefficient
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-67 kcal/mol
Surface area23620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.910, 49.910, 264.377
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#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
#2: Chemical ChemComp-ERP / 6-[([1,1'-biphenyl]-4-yl)ethynyl]-9-beta-D-ribofuranosyl-9H-purine


Mass: 428.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H20N4O4
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.39 Å3/Da / Density % sol: 48.45 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 100 mM Bis-Tris, pH 6.5, 2.0 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: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 24, 2017
RadiationMonochromator: double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.23→35.29 Å / Num. obs: 31259 / % possible obs: 98.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.06034 / Net I/σ(I): 26.43
Reflection shellResolution: 2.23→2.31 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.1671 / Mean I/σ(I) obs: 10.31 / % possible all: 98.3

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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: 2.23→35.29 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.8
RfactorNum. reflection% reflection
Rfree0.235 1532 4.95 %
Rwork0.199 --
obs0.201 30941 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.23→35.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4675 0 76 207 4958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084839
X-RAY DIFFRACTIONf_angle_d0.7126584
X-RAY DIFFRACTIONf_dihedral_angle_d15.2062786
X-RAY DIFFRACTIONf_chiral_restr0.057759
X-RAY DIFFRACTIONf_plane_restr0.003850
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2301-2.30210.30381550.25282614X-RAY DIFFRACTION98
2.3021-2.38430.26251580.23652720X-RAY DIFFRACTION100
2.3843-2.47980.27681420.22552702X-RAY DIFFRACTION100
2.4798-2.59260.2431330.2162655X-RAY DIFFRACTION99
2.5926-2.72930.30631600.22292651X-RAY DIFFRACTION99
2.7293-2.90020.30481370.23062690X-RAY DIFFRACTION100
2.9002-3.1240.24241330.23462718X-RAY DIFFRACTION100
3.124-3.43810.27951340.21652662X-RAY DIFFRACTION99
3.4381-3.93510.19881100.18662729X-RAY DIFFRACTION99
3.9351-4.95560.20051280.16042700X-RAY DIFFRACTION99
4.9556-35.29610.19361420.182568X-RAY DIFFRACTION95

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