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- PDB-2mo5: hIFABP-oleate complex -

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Basic information

Entry
Database: PDB / ID: 2mo5
TitlehIFABP-oleate complex
ComponentsFatty acid-binding protein, intestinal
KeywordsTRANSPORT PROTEIN / Protein-ligand complex / Intestinal Fatty Acid Binding Protein / human IFABP / Human FABP2
Function / homology
Function and homology information


intestinal lipid absorption / apical cortex / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / Triglyceride catabolism / microvillus / fatty acid transport / fatty acid metabolic process / fatty acid binding / nucleus / cytosol
Similarity search - Function
Fatty acid-binding protein, intestinal / Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Lipocalin/cytosolic fatty-acid binding domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
OLEIC ACID / Fatty acid-binding protein, intestinal
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model1
AuthorsPatil, R. / Mohanty, B. / Headey, S. / Porter, C. / Scanlon, M.
CitationJournal: To be Published
Title: Structure of oleate bound human intestinal fatty acid binding protein
Authors: Patil, R. / Mohanty, B. / Headey, S. / Porter, C. / Scanlon, M.
History
DepositionApr 17, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)16,6662
Polymers16,3831
Non-polymers2821
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Fatty acid-binding protein, intestinal / Fatty acid-binding protein 2 / Intestinal-type fatty acid-binding protein / I-FABP


Mass: 16383.419 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP2, FABPI / Plasmid: pET-45b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: P12104
#2: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-13C NOESY aromatic
1213D 1H-13C NOESY aliphatic
1313D 1H-15N NOESY
1412D 1H-15N HSQC
1512D 1H-13C HSQC
1613D HN(CA)CB
1713D HNCA
1813D CBCA(CO)NH
1932D 1H-13C HSQC
110313C HMQC TOCSY
11122D 1H-13C HSQC
11213D (H)CC(CO)NH
11313D hCC(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] hIFABP, 2.5 mM oleic acid, 50 mM sodium chloride, 20 mM MES, 0.5% methanol, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 13C] oleic acid, 50 mM sodium chloride, 20 mM MES, 0.5 mM ethanol, 90% H2O/10% D2O90% H2O/10% D2O
30.8 mM [U-100% 15N] hIFABP, 2 mM [U-100% 13C] oleic acid, 50 mM sodium chloride, 20 mM MES, 0.5 % methanol, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMhIFABP-1[U-100% 13C; U-100% 15N]1
2.5 mMoleic acid-21
50 mMsodium chloride-31
20 mMMES-41
0.5 %methanol-51
0.5 mMoleic acid-6[U-100% 13C]2
50 mMsodium chloride-72
20 mMMES-82
0.5 mMethanol-92
0.8 mMhIFABP-10[U-100% 15N]3
2 mMoleic acid-11[U-100% 13C]3
50 mMsodium chloride-123
20 mMMES-133
0.5 %methanol-143
Sample conditionspH: 5.5 / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
TopSpinBruker Biospindata analysis
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichdata analysis
CARAKeller and Wuthrichchemical shift calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2878 / NOE intraresidue total count: 593 / NOE long range total count: 979 / NOE medium range total count: 532 / NOE sequential total count: 774 / Protein phi angle constraints total count: 117 / Protein psi angle constraints total count: 115
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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