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- PDB-7fbf: The 0.86 angstrom X-ray structure of the human heart fatty acid-b... -

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Basic information

Entry
Database: PDB / ID: 7fbf
TitleThe 0.86 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with octanoic acid
ComponentsFatty acid-binding protein, heart
KeywordsLIPID BINDING PROTEIN / FABP / Complex / Binding protein / octanoic acid
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 / cytoskeletal protein binding / brown fat cell differentiation / cholesterol homeostasis / fatty acid metabolic process / response to insulin / response to xenobiotic stimulus / negative regulation of cell population proliferation / : / 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
OCTANOIC ACID (CAPRYLIC ACID) / Fatty acid-binding protein, heart
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.86 Å
AuthorsSugiyama, S. / Kakinouchi, K. / Matsuoka, S. / Tsuchikawa, H. / Sonoyama, M. / Inoue, Y. / Hayashi, F. / Murata, M.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJTM19DC Japan
Japan Society for the Promotion of Science (JSPS)19K06588 Japan
Japan Science and TechnologyJPMJER1005 Japan
CitationJournal: Int.J.Biol.Macromol. / Year: 2026
Title: Intermolecular interactions of perfluoroalkyl acids with human heart-type fatty acid-binding protein.
Authors: Maekawa, S. / Takamiya, N. / Terawaki, H. / Kondo, N. / Hayashi, F. / Shimoaka, T. / Matsuoka, S. / Matsumori, N. / Murata, M. / Sonoyama, M. / Sugiyama, S.
History
DepositionJul 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jun 24, 2026Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,3063
Polymers14,8791
Non-polymers4272
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint-1 kcal/mol
Surface area7500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.566, 69.740, 33.911
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fatty acid-binding protein, heart / Fatty acid-binding protein 3 / Heart-type fatty acid-binding protein / H-FABP / Mammary-derived ...Fatty acid-binding protein 3 / Heart-type fatty acid-binding protein / H-FABP / Mammary-derived growth inhibitor / MDGI / Muscle fatty acid-binding protein / M-FABP


Mass: 14879.022 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP3, FABP11, MDGI / Production host: Escherichia coli (E. coli) / References: UniProt: P05413
#2: Chemical ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID)


Mass: 144.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Tris-HCl (pH8.5), 60% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.8 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.86→50 Å / Num. obs: 107983 / % possible obs: 97.9 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 11.3
Reflection shellResolution: 0.86→0.87 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3 / Num. unique obs: 5291

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TJZ

4tjz


Resolution: 0.86→22.22 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.308 / SU ML: 0.008 / Cross valid method: THROUGHOUT / ESU R: 0.014 / ESU R Free: 0.013 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12323 5380 5 %RANDOM
Rwork0.11847 ---
obs0.11871 102346 97.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.391 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å2-0 Å20 Å2
2--0.27 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 0.86→22.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1038 0 29 221 1288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0131302
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171270
X-RAY DIFFRACTIONr_angle_refined_deg2.2931.6681769
X-RAY DIFFRACTIONr_angle_other_deg1.6161.6192973
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8585172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.6823.62158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84215249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.084156
X-RAY DIFFRACTIONr_chiral_restr0.1110.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021485
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02257
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2340.742640
X-RAY DIFFRACTIONr_mcbond_other2.2280.741639
X-RAY DIFFRACTIONr_mcangle_it3.1131.112828
X-RAY DIFFRACTIONr_mcangle_other3.1121.113829
X-RAY DIFFRACTIONr_scbond_it1.5420.897662
X-RAY DIFFRACTIONr_scbond_other1.5410.898662
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8981.286942
X-RAY DIFFRACTIONr_long_range_B_refined3.80710.6851431
X-RAY DIFFRACTIONr_long_range_B_other2.9969.5871373
X-RAY DIFFRACTIONr_rigid_bond_restr15.58232572
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 0.86→0.882 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 397 -
Rwork0.208 7346 -
obs--95.71 %

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