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- PDB-2obu: Solution structure of GIP in TFE/water -

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Basic information

Entry
Database: PDB / ID: 2obu
TitleSolution structure of GIP in TFE/water
ComponentsGastric inhibitory polypeptide
KeywordsHORMONE/GROWTH FACTOR / GIP / NMR / MOLECULAR MODELLING / HELIX / DIABETES / OBESITY / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


gastric inhibitory polypeptide receptor binding / digestive system development / gastric inhibitory peptide signaling pathway / glucagon receptor binding / regulation of fatty acid biosynthetic process / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / endocrine pancreas development / response to selenium ion / response to acidic pH / positive regulation of glucose transmembrane transport ...gastric inhibitory polypeptide receptor binding / digestive system development / gastric inhibitory peptide signaling pathway / glucagon receptor binding / regulation of fatty acid biosynthetic process / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / endocrine pancreas development / response to selenium ion / response to acidic pH / positive regulation of glucose transmembrane transport / triglyceride homeostasis / exploration behavior / response to lipid / response to starvation / regulation of insulin secretion / response to axon injury / response to amino acid / positive regulation of cAMP-mediated signaling / response to glucose / sensory perception of pain / adult locomotory behavior / female pregnancy / long-term synaptic potentiation / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / response to organic cyclic compound / hormone activity / memory / response to peptide hormone / Glucagon-type ligand receptors / G alpha (s) signalling events / secretory granule lumen / response to xenobiotic stimulus / endoplasmic reticulum lumen / neuronal cell body / signal transduction / extracellular space / extracellular region
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #590 / Gastric inhibitory polypeptide / Glucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
Gastric inhibitory polypeptide
Similarity search - Component
MethodSOLUTION NMR / torsion angle dynamics
AuthorsAlana, I. / Malthouse, J.P.G. / O'Harte, F.P.M. / Hewage, C.M.
CitationJournal: Proteins / Year: 2007
Title: The bioactive conformation of glucose-dependent insulinotropic polypeptide by NMR and CD spectroscopy
Authors: Alana, I. / Malthouse, J.P.G. / O'harte, F.P.M. / Hewage, C.M.
History
DepositionDec 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gastric inhibitory polypeptide


Theoretical massNumber of molelcules
Total (without water)4,9911
Polymers4,9911
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1

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Components

#1: Protein/peptide Gastric inhibitory polypeptide / / GIP / Glucose-dependent insulinotropic polypeptide


Mass: 4990.586 Da / Num. of mol.: 1 / Fragment: RESIDUES 52-93 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans, gene GIP / References: UniProt: P09681

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D TOCSY
1312D NOESY

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Sample preparation

DetailsContents: GIP, 50% TFE-D3, 50% H2O
Sample conditionspH: 3.0 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX8002
Bruker DRXBrukerDRX9003

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Processing

NMR software
NameVersionDeveloperClassification
SYBYL6.8.1TRIPOSrefinement
XwinNMR3.5collection
XwinNMR3.5processing
Sparky3.11data analysis
CYANA1.0.6structure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 640 RESTRAINTS, 631 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 9 DIHEDRAL ANGLE RESTRAINTS
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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