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- PDB-6do7: NMR solution structure of wild type hFABP1 with GW7647 -

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Basic information

Entry
Database: PDB / ID: 6do7
TitleNMR solution structure of wild type hFABP1 with GW7647
ComponentsFatty acid-binding protein, liver
KeywordsLIPID BINDING PROTEIN
Function / homology
Function and homology information


response to vitamin B3 / oleic acid binding / apical cortex / positive regulation of fatty acid beta-oxidation / bile acid binding / intestinal absorption / Heme degradation / long-chain fatty acid transmembrane transporter activity / heterocyclic compound binding / Triglyceride catabolism ...response to vitamin B3 / oleic acid binding / apical cortex / positive regulation of fatty acid beta-oxidation / bile acid binding / intestinal absorption / Heme degradation / long-chain fatty acid transmembrane transporter activity / heterocyclic compound binding / Triglyceride catabolism / antioxidant activity / peroxisomal matrix / fatty acid transport / Regulation of lipid metabolism by PPARalpha / fatty acid binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PPARA activates gene expression / Cytoprotection by HMOX1 / phospholipid binding / cellular response to hydrogen peroxide / cellular response to hypoxia / chromatin binding / negative regulation of apoptotic process / protein-containing complex / extracellular exosome / nucleoplasm / 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
Fatty acid-binding protein, liver
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics / Restraint energy minimization
AuthorsScanlon, M.J. / Mohanty, B. / Doak, B.C. / Patil, R.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP120102930 Australia
Australian Research Council (ARC)DP150102587 Australia
CitationJournal: J. Biol. Chem. / Year: 2019
Title: A ligand-induced structural change in fatty acid-binding protein 1 is associated with potentiation of peroxisome proliferator-activated receptor alpha agonists.
Authors: Patil, R. / Mohanty, B. / Liu, B. / Chandrashekaran, I.R. / Headey, S.J. / Williams, M.L. / Clements, C.S. / Ilyichova, O. / Doak, B.C. / Genissel, P. / Weaver, R.J. / Vuillard, L. / Halls, ...Authors: Patil, R. / Mohanty, B. / Liu, B. / Chandrashekaran, I.R. / Headey, S.J. / Williams, M.L. / Clements, C.S. / Ilyichova, O. / Doak, B.C. / Genissel, P. / Weaver, R.J. / Vuillard, L. / Halls, M.L. / Porter, C.J.H. / Scanlon, M.J.
History
DepositionJun 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fatty acid-binding protein, liver


Theoretical massNumber of molelcules
Total (without water)15,2251
Polymers15,2251
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8480 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 40structures with acceptable covalent geometry
RepresentativeModel #1closest to the average

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Components

#1: Protein Fatty acid-binding protein, liver / Fatty acid-binding protein 1 / Liver-type fatty acid-binding protein / L-FABP


Mass: 15225.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP1, FABPL / Production host: Escherichia coli (E. coli) / References: UniProt: P07148

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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
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HNCA
151isotropic13D HN(CA)CB
171isotropic13D CBCA(CO)NH
161isotropic23D 15N resolved [1H,1H]-NOESY
191isotropic23D 13Caliphatic resolved [1H,1H]-NOESY
181isotropic23D 13Caromatic resolved [1H,1H]-NOESY

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Sample preparation

DetailsType: solution
Contents: 20 mM sodium phosphate, 50 mM sodium chloride, 0.5 mM [U-13C; U-15N] Human liver fatty acid binding protein (hFABP1), 90% H2O/10% D2O
Details: 0.5 mM protein, 20 mM Sodium Phosphate, 50 mM NaCl, pH 5.5
Label: 15N13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
0.5 mMHuman liver fatty acid binding protein (hFABP1)[U-13C; U-15N]1
Sample conditionsDetails: 0.5 mM protein, 20 mM Sodium Phosphate, 50 mM NaCl, pH 5.5
Ionic strength: 20 mM Sodium Phosphate, 50 mM NaCl mM / Label: conditions_1 / pH: 5.5 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
UNIO10-ATNOS/CANID2.0.2Dr. Torsten Herrmannstructure calculation
OPALpKoradi et al, 2000refinement
PrimePrime, Schrodinger, LLC, New York, NY, 2018refinement
Refinement
MethodSoftware ordinalDetails
molecular dynamics8the structures are based on a total of 2553 NOE-derived distance constraints, 202 dihedral angle constraints, 58 distance restraints from hydrogen bonds
Restraint energy minimization7OPALp
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 40 / Conformers submitted total number: 10

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