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- PDB-6c9n: Mycobacterium tuberculosis adenosine kinase bound to sangivamycin -

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Basic information

Entry
Database: PDB / ID: 6c9n
TitleMycobacterium tuberculosis adenosine kinase bound to sangivamycin
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
SANGIVAMYCIN / Adenosine kinase / Adenosine kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,57511
Polymers69,0082
Non-polymers1,5679
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Sedimentation coefficient
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-44 kcal/mol
Surface area23590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.910, 48.910, 262.059
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, 250 molecules

#2: Chemical
ChemComp-SGV / SANGIVAMYCIN / 4-amino-7-beta-D-ribofuranosyl-7H-pyrrolo[2,3-d]pyrimidine-5-carboxamide


Mass: 309.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H15N5O5 / Comment: inhibitor*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.27 Å3/Da / Density % sol: 45.84 %
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: 19-ID / Wavelength: 0.9791829 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791829 Å / Relative weight: 1
ReflectionResolution: 2.1→34.58 Å / Num. obs: 35090 / % possible obs: 98.26 % / Redundancy: 7.3 % / Biso Wilson estimate: 34.5 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 22.89
Reflection shellResolution: 2.1→2.175 Å / Rmerge(I) obs: 0.245 / Num. unique obs: 3541 / % possible all: 99.75

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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: 2.1→34.585 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2306 1748 4.99 %
Rwork0.1866 --
obs0.1887 35004 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→34.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4660 0 88 241 4989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114833
X-RAY DIFFRACTIONf_angle_d1.0996579
X-RAY DIFFRACTIONf_dihedral_angle_d14.0862780
X-RAY DIFFRACTIONf_chiral_restr0.06757
X-RAY DIFFRACTIONf_plane_restr0.008849
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1004-2.16220.25981630.19582759X-RAY DIFFRACTION100
2.1622-2.23190.29711610.19722863X-RAY DIFFRACTION100
2.2319-2.31170.24861200.20072796X-RAY DIFFRACTION100
2.3117-2.40420.26441400.19882794X-RAY DIFFRACTION100
2.4042-2.51360.26251760.1962767X-RAY DIFFRACTION100
2.5136-2.64610.25111610.18842817X-RAY DIFFRACTION100
2.6461-2.81180.23811540.192813X-RAY DIFFRACTION100
2.8118-3.02880.26531520.20332827X-RAY DIFFRACTION100
3.0288-3.33340.23551300.2022787X-RAY DIFFRACTION99
3.3334-3.81520.19791260.18272672X-RAY DIFFRACTION94
3.8152-4.80470.22011210.15842601X-RAY DIFFRACTION92
4.8047-34.58930.19931440.18832760X-RAY DIFFRACTION97

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