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- PDB-6c9q: Mycobacterium tuberculosis adenosine kinase bound to 5'-aminoadenosine -

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Basic information

Entry
Database: PDB / ID: 6c9q
TitleMycobacterium tuberculosis adenosine kinase bound to 5'-aminoadenosine
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
5'-amino-5'-deoxyadenosine / Adenosine kinase / Adenosine kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6622
Polymers35,3961
Non-polymers2661
Water3,711206
1
A: Adenosine kinase
hetero molecules

A: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3244
Polymers70,7922
Non-polymers5332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area4580 Å2
ΔGint-28 kcal/mol
Surface area24370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.904, 71.904, 110.256
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Adenosine kinase / AK


Mass: 35395.898 Da / Num. of mol.: 1
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-5N5 / 5'-amino-5'-deoxyadenosine


Mass: 266.257 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.34 Å3/Da / Density % sol: 47.49 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 100 mM HEPES, pH 7.5, 1.2 M sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793371 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 21, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793371 Å / Relative weight: 1
ReflectionResolution: 1.95→41.28 Å / Num. obs: 24597 / % possible obs: 99.82 % / Redundancy: 10.7 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.07494 / Net I/σ(I): 40.22
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.1639 / Mean I/σ(I) obs: 17.16 / Num. unique obs: 26310 / % possible all: 99.92

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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: 1.95→41.277 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2082 1198 4.87 %
Rwork0.1836 --
obs0.1848 24591 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→41.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2483 0 19 206 2708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092553
X-RAY DIFFRACTIONf_angle_d0.993474
X-RAY DIFFRACTIONf_dihedral_angle_d19.181504
X-RAY DIFFRACTIONf_chiral_restr0.053400
X-RAY DIFFRACTIONf_plane_restr0.006450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9503-2.02830.23951230.21942556X-RAY DIFFRACTION100
2.0283-2.12070.24391270.20272576X-RAY DIFFRACTION100
2.1207-2.23250.20681050.19952584X-RAY DIFFRACTION100
2.2325-2.37230.24441450.20532559X-RAY DIFFRACTION100
2.3723-2.55550.24041590.19792557X-RAY DIFFRACTION100
2.5555-2.81260.2211460.18652571X-RAY DIFFRACTION100
2.8126-3.21940.22691440.1882605X-RAY DIFFRACTION100
3.2194-4.05560.17521340.15942629X-RAY DIFFRACTION100
4.0556-41.2860.17871150.17222756X-RAY DIFFRACTION99

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