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

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Basic information

Entry
Database: PDB / ID: 6drg
TitleNMR solution structure of wild type hFABP1 with GW7647
ComponentsFatty acid-binding protein, liver
KeywordsLIPID BINDING PROTEIN / hLFABP / GW7647
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 / antioxidant activity ...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 / antioxidant activity / Triglyceride catabolism / peroxisomal matrix / fatty acid transport / Regulation of lipid metabolism by PPARalpha / fatty acid binding / phospholipid binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PPARA activates gene expression / Cytoprotection by HMOX1 / 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
Chem-2VN / Fatty acid-binding protein, liver
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / 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 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2018Provider: 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
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty acid-binding protein, liver
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7282
Polymers15,2251
Non-polymers5031
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8310 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 40structures with acceptable covalent geometry
RepresentativeModel #1fewest violations

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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
#2: Chemical ChemComp-2VN / 2-[(4-{2-[(4-cyclohexylbutyl)(cyclohexylcarbamoyl)amino]ethyl}phenyl)sulfanyl]-2-methylpropanoic acid


Mass: 502.752 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H46N2O3S

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic22D 1H-13C HSQC
131isotropic23D 15N-resolved [1H,1H]-NOESY
141isotropic23D 13Cali resolved [1H,1H]-NOESY
151isotropic23D 13Caro resolved [1H,1H]-NOESY
161isotropic22D F1-edited, F2-13C,15N-filtered [1H,1H] NOESY
171isotropic23D F1-13C,15N-filtered, F2-13Cali edited [1H,1H] NOESY
182isotropic12D 1H-15N HSQC
192isotropic12D F1, F2-13C,15N-filtered [1H,1H] NOESY
1102isotropic12D F1-edited, F2-13C,15N-filtered [1H,1H] NOESY
1112isotropic13D F1-13C,15N-filtered, F2-15N edited [1H,1H] NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.5 mM [U-15N13C] hFABP1 wild type, 0.5 mM GW7647, 20 mM sodium phosphate, 50 mM sodium chloride, 1 % D6 DMSO, 90% H2O/10% D2O0.5 mM [U-15N13C]-labelled hFABP1 wild type; 20 mM sodium phosphate; 50 mM NaCl; pH 5.5;1 mM GW7647; 1% D6-DMSO[U-15N13C]-labelled hFABP190% H2O/10% D2O
solution21 mM [U-2H,15N13C] hFABP1 wild type, 1 mM GW7647, 50 mM sodium chloride, 20 mM sodium phosphate, 1 % D6 DMSO, 90% H2O/10% D2O1 mM [U-2H,15N13C]-labelled hFABP1 wild type; 20 mM sodium phosphate; 50 mM NaCl; pH 5.5; 1 mM GW7647; 1% D6-DMSO[U-2H,15N13C]-labelled hFABP190% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMhFABP1 wild type[U-15N13C]1
0.5 mMGW7647natural abundance1
20 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
1 %DMSOD61
1 mMhFABP1 wild type[U-2H,15N13C]2
1 mMGW7647natural abundance2
50 mMsodium chloridenatural abundance2
20 mMsodium phosphatenatural abundance2
1 %DMSOD62
Sample conditionsIonic strength: 20 mM sodium phosphate and 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
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
PrimePrime, Schrodinger, LLC, New York, NY, 2018refinement
OPALpKoradi et al, 2000refinement
RefinementMethod: restraint energy minimization / Software ordinal: 7 / Details: OPALp
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 40 / Conformers submitted total number: 10

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