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- PDB-2kxk: Human Insulin Mutant A22Gly-B31Lys-B32Arg -

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Basic information

Entry
Database: PDB / ID: 2kxk
TitleHuman Insulin Mutant A22Gly-B31Lys-B32Arg
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / Human Insulin / Mutant / water/acetonitrile solution
Function / homology
Function and homology information


negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / negative regulation of feeding behavior / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / negative regulation of feeding behavior / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / Regulation of gene expression in beta cells / negative regulation of acute inflammatory response / positive regulation of protein autophosphorylation / alpha-beta T cell activation / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of glycogen biosynthetic process / Signal attenuation / fatty acid homeostasis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of insulin receptor signaling pathway / negative regulation of lipid catabolic process / regulation of protein localization to plasma membrane / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / activation of protein kinase B activity / COPI-mediated anterograde transport / transport vesicle / nitric oxide-cGMP-mediated signaling / negative regulation of reactive oxygen species biosynthetic process / Insulin receptor recycling / insulin-like growth factor receptor binding / positive regulation of brown fat cell differentiation / NPAS4 regulates expression of target genes / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of nitric-oxide synthase activity / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / regulation of transmembrane transporter activity / positive regulation of glycolytic process / positive regulation of long-term synaptic potentiation / positive regulation of cytokine production / endosome lumen / acute-phase response / positive regulation of D-glucose import / positive regulation of protein secretion / positive regulation of cell differentiation / Regulation of insulin secretion / insulin receptor binding / wound healing / negative regulation of protein catabolic process / hormone activity / regulation of synaptic plasticity / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / cognition / glucose metabolic process / vasodilation / insulin receptor signaling pathway / glucose homeostasis / cell-cell signaling / regulation of protein localization / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protease binding / positive regulation of cell growth / secretory granule lumen / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / positive regulation of cell migration / G protein-coupled receptor signaling pathway / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / regulation of DNA-templated transcription / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsBocian, W. / Kozerski, L.
CitationJournal: To be Published
Title: Novel recombinant insulin analogue with flexible C - terminus in B chain. NMR structure of biosynthetic engineered A22G-B31K-B32R human insulin monomer in water /acetonitrile solution.
Authors: Borowicz, P. / Mikolajczyk, J. / Bocian, W. / Sitkowski, J. / Bednarek, E. / Jaworska, D. / Blazej, S. / Bogiel, M. / Mikiewicz-Sygula, D. / Kurzynoga, D. / Kozerski, L.
History
DepositionMay 7, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin A chain
B: Insulin B chain


Theoretical massNumber of molelcules
Total (without water)6,1612
Polymers6,1612
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Insulin A chain


Mass: 2440.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Escherichia coli (E. coli) / References: UniProt: P01308
#2: Protein/peptide Insulin B chain


Mass: 3720.326 Da / Num. of mol.: 1 / Mutation: R31K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Escherichia coli (E. coli) / References: UniProt: P01308
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1322D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
12.5 mM protein_1 and protein_2-1, 65% H2O / 35% CD3CN65% H2O / 35% CD3CN
22.5 mM protein_1 and protein_2-2, 65% D2O / 35% CD3CN65% D2O / 35% CD3CN
Sample
Conc. (mg/ml)ComponentSolution-ID
2.5 mMentity_1 and entity_2-11
2.5 mMentity_1 and entity_2-22
Sample conditionsIonic strength: 0 / pH: 3.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian Uniform NMR System / Manufacturer: Varian / Model: Uniform NMR System / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
Sparky2.6Goddardchemical shift assignment
VnmrJ2.2CVariancollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 700 / NOE intraresidue total count: 230 / NOE long range total count: 35 / NOE medium range total count: 150 / NOE sequential total count: 235 / Protein chi angle constraints total count: 159 / Protein phi angle constraints total count: 37 / Protein psi angle constraints total count: 37
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 1.15 Å / Representative conformer: 1

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