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- PDB-1g5w: SOLUTION STRUCTURE OF HUMAN HEART-TYPE FATTY ACID BINDING PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1g5w
TitleSOLUTION STRUCTURE OF HUMAN HEART-TYPE FATTY ACID BINDING PROTEIN
ComponentsFATTY ACID-BINDING PROTEIN
KeywordsLIPID BINDING PROTEIN / NMR spectroscopy / protein-ligand interactions / selected-fit binding
Function / homology
Function and homology information


icosatetraenoic acid binding / positive regulation of long-chain fatty acid import into cell / regulation of phosphatidylcholine biosynthetic process / regulation of fatty acid oxidation / oleic acid binding / positive regulation of phospholipid biosynthetic process / intracellular lipid transport / response to fatty acid / phospholipid homeostasis / long-chain fatty acid transmembrane transporter activity ...icosatetraenoic acid binding / positive regulation of long-chain fatty acid import into cell / regulation of phosphatidylcholine biosynthetic process / regulation of fatty acid oxidation / oleic acid binding / positive regulation of phospholipid biosynthetic process / intracellular lipid transport / response to fatty acid / phospholipid homeostasis / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / Triglyceride catabolism / sarcoplasm / long-chain fatty acid transport / brown fat cell differentiation / cytoskeletal protein binding / cholesterol homeostasis / fatty acid metabolic process / response to insulin / response to xenobiotic stimulus / negative regulation of cell population proliferation / extracellular space / extracellular exosome / nucleus / cytosol
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Fatty acid-binding protein, heart
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, energy-minimization
AuthorsLuecke, C. / Rademacher, M. / Zimmerman, A. / van Moerkerk, H.T.B. / Veerkamp, J.H. / Rueterjans, H.
Citation
Journal: Biochem.J. / Year: 2001
Title: Spin-system heterogeneities indicate a selected-fit mechanism in fatty acid binding to heart-type fatty acid-binding protein (H-FABP).
Authors: Lucke, C. / Rademacher, M. / Zimmerman, A.W. / van Moerkerk, H.T. / Veerkamp, J.H. / Ruterjans, H.
#1: Journal: J.Biol.Chem. / Year: 1992
Title: Three-dimensional structure of recombinant human muscle fatty acid-binding protein
Authors: Zanotti, G. / Scapin, G. / Spandon, P. / Veerkamp, J.H. / Sacchettini, J.C.
#2: Journal: Structure / Year: 1994
Title: Structural studies on human muscle fatty acid-binding protein at 1.4 A resolution: binding interactions with three C18 fatty acids
Authors: Young, A.C.M. / Scapin, G. / Kromminga, A. / Patel, S.B. / Veerkamp, J.H. / Sacchettini, J.C.
#3: Journal: Eur.J.Biochem. / Year: 1995
Title: Three-dimensional structure of bovine heart fatty-acid-binding protein with bound palmitic acid, determined by multidimensional NMR spectroscopy
Authors: Lassen, D. / Luecke, C. / Kveder, M. / Mesgarzadeh, A. / Schmidt, J.M. / Specht, B. / Lezius, A. / Spener, F. / Rueterjans, H.
History
DepositionNov 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 1.4May 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: FATTY ACID-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)14,7481
Polymers14,7481
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 lowest violations of experimental constraints
Representative

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Components

#1: Protein FATTY ACID-BINDING PROTEIN


Mass: 14747.825 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: MUSCLE / Gene: FABP3 / Organ: HEART / Plasmid: PET3D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P05413

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1223D 15N-separated NOESY
NMR detailsText: This structure was determined using non-delipidated recombinant human H-FABP samples.

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Sample preparation

Details
Solution-IDContentsSolvent system
11-3 mM H-FABP (non-labelled or 15N-labelled); 20 mM phosphate buffer (pH 5.5); 0.05% NaN390% H2O/10% D2O
21-3 mM H-FABP (U-15N); 20 mM phosphate buffer (pH 5.5); 0.05% NaN390% H2O/10% D2O
Sample conditionsIonic strength: 20 / pH: 5.5 / Pressure: ambient / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.3BRUKERprocessing
AURELIA2.5.9BRUKERdata analysis
DYANA1.5P. Guentertstructure solution
Discover97MSIrefinement
RefinementMethod: simulated annealing, energy-minimization / Software ordinal: 1
Details: The structure was determined based on 2589 NOE-derived distance constraints and 40 H-bond constraints.
NMR ensembleConformer selection criteria: structures with lowest violations of experimental constraints
Conformers calculated total number: 100 / Conformers submitted total number: 20

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