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- PDB-7x7s: Solution structure of human adenylate kinase 1 (hAK1) -

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Basic information

Entry
Database: PDB / ID: 7x7s
TitleSolution structure of human adenylate kinase 1 (hAK1)
ComponentsAdenylate kinase isoenzyme 1
KeywordsTRANSFERASE / Adenylate kinase / ADP / ATP / LID domain
Function / homology
Function and homology information


nucleoside-triphosphate-adenylate kinase / outer dense fiber / nucleoside triphosphate adenylate kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / (d)CMP kinase activity / adenylate kinase / adenylate kinase activity / nucleoside-diphosphate kinase ...nucleoside-triphosphate-adenylate kinase / outer dense fiber / nucleoside triphosphate adenylate kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / (d)CMP kinase activity / adenylate kinase / adenylate kinase activity / nucleoside-diphosphate kinase / nucleobase-containing small molecule interconversion / Interconversion of nucleotide di- and triphosphates / nucleoside diphosphate kinase activity / ATP metabolic process / phosphorylation / extracellular exosome / ATP binding / cytoplasm / cytosol
Similarity search - Function
Adenylate kinase isoenzyme 1 / Adenylate kinase, isozyme 1/5 / Adenylate kinase / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Adenylate kinase isoenzyme 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsZhang, H.
Funding support China, 1items
OrganizationGrant numberCountry
Natural Science Foundation of Fujian Province2011J01246 China
CitationJournal: Biomolecules / Year: 2022
Title: ADP-Induced Conformational Transition of Human Adenylate Kinase 1 Is Triggered by Suppressing Internal Motion of alpha 3 alpha 4 and alpha 7 alpha 8 Fragments on the ps-ns Timescale.
Authors: Guo, C. / Zhang, H. / Lin, W. / Chen, H. / Chang, T. / Wu, Z. / Yu, J. / Lin, D.
History
DepositionMar 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenylate kinase isoenzyme 1


Theoretical massNumber of molelcules
Total (without water)22,0791
Polymers22,0791
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9840 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Adenylate kinase isoenzyme 1 / AK 1 / ATP-AMP transphosphorylase 1 / ATP:AMP phosphotransferase / Adenylate monophosphate kinase / Myokinase


Mass: 22079.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AK1 / Production host: Escherichia coli (E. coli)
References: UniProt: P00568, adenylate kinase, nucleoside-diphosphate kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic13D HN(CA)CB
132isotropic13D CBCA(CO)NH
142isotropic13D HNCA
152isotropic13D HN(CO)CA
162isotropic13D HNCO
172isotropic13D 1H-15N TOCSY
182isotropic13D HBHA(CO)NH
192isotropic13D (H)CCH-TOCSY
1102isotropic13D C(CO)NH
1112isotropic13D 1H-13C NOESY
1122isotropic13D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM [U-100% 15N] hAK1, 10 mM Na2HPO4, 50 mM NaCl, 100 mM Na2SO4, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution21.0 mM [U-100% 13C; U-100% 15N] hAK1, 10 mM Na2HPO4, 50 mM NaCl, 100 mM Na2SO4, 90% H2O/10% D2O13C/15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMhAK1[U-100% 15N]1
10 mMNa2HPO4natural abundance1
50 mMNaClnatural abundance1
100 mMNa2SO4natural abundance1
1.0 mMhAK1[U-100% 13C; U-100% 15N]2
10 mMNa2HPO4natural abundance2
50 mMNaClnatural abundance2
100 mMNa2SO4natural abundance2
Sample conditionsIonic strength: 160 mM / Label: NMR_condition / pH: 6.2 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRFAM-SPARKYLee W., et al.chemical shift assignment
ARIA2alphaRieping W., Linge, J. P., et al.structure calculation
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 20

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