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- PDB-1eio: ILEAL LIPID BINDING PROTEIN IN COMPLEX WITH GLYCOCHOLATE -

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Basic information

Entry
Database: PDB / ID: 1eio
TitleILEAL LIPID BINDING PROTEIN IN COMPLEX WITH GLYCOCHOLATE
ComponentsILEAL LIPID BINDING PROTEIN
KeywordsLIPID BINDING PROTEIN / bile acid binding / protein-ligand interaction / LIPID-BINDING PROTEIN
Function / homology
Function and homology information


fatty acid transport / fatty acid binding / membrane / nucleus / cytosol
Similarity search - Function
Lipocalin / cytosolic fatty-acid binding protein family / Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
GLYCOCHOLIC ACID / Gastrotropin
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsLuecke, C. / Zhang, F. / Hamilton, J.A. / Sacchettini, J.C. / Rueterjans, H.
Citation
Journal: Eur.J.Biochem. / Year: 2000
Title: Solution structure of ileal lipid binding protein in complex with glycocholate.
Authors: Luecke, C. / Zhang, F. / Hamilton, J.A. / Sacchettini, J.C. / Rueterjans, H.
#1: Journal: Structure / Year: 1996
Title: Flexibility is a likely determinant of binding in the case of Ileal Lipid Binding Protein
Authors: Luecke, C. / Zhang, F. / Rueterjans, H. / Hamilton, J.A. / Sacchettini, J.C.
#2: Journal: Mol.Cell.Biochem. / Year: 1999
Title: A comparative study of the backbone dynamics of two closely related lipid binding proteins: bovine heart Fatty Acid Binding Protein and porcine Ileal Lipid Binding Protein
Authors: Luecke, C. / Fushman, D. / Ludwig, C. / Hamilton, J.A. / Sacchettini, J.C. / Rueterjans, H.
History
DepositionFeb 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_keywords.text / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: 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: ILEAL LIPID BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5602
Polymers14,0941
Non-polymers4661
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)5 / 8structures with the lowest energies after docking of ligand
RepresentativeModel #1lowest energy

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Components

#1: Protein ILEAL LIPID BINDING PROTEIN


Mass: 14093.877 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Plasmid: PET3D / Production host: Escherichia coli (E. coli) / References: UniProt: P10289
#2: Chemical ChemComp-GCH / GLYCOCHOLIC ACID / N-CHOLYLGLYCINE


Mass: 465.623 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H43NO6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D 1H/13C-NOESY
1312D TOCSY

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Sample preparation

DetailsContents: 3-4mM ILBP/glycocholate complex
Solvent system: 20mM phosphate; 0.05% azide; 90% H2O, 10% D2O
Sample conditionsIonic strength: 20mM KH2PO4 / pH: 5.0 / Pressure: ambient / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002
Bruker DRXBrukerDRX8003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.3Brukercollection
AURELIA2.1Brukerdata analysis
Felix95MSIdata analysis
DIANA2.8Guenthertstructure solution
SYBYL6.4Triposrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: the ligand was docked into the protein structure by simulated annealing
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energies after docking of ligand
Conformers calculated total number: 8 / Conformers submitted total number: 5

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