7WPG | pdb_00007wpg

The 0.90 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with heptanoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.90 Å
  • R-Value Free: 
    0.126 (Depositor), 0.135 (DCC) 
  • R-Value Work: 
    0.113 (Depositor), 0.120 (DCC) 
  • R-Value Observed: 
    0.114 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7WPG

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Intermolecular interactions of perfluoroalkyl acids with human heart-type fatty acid-binding protein.

Maekawa, S.Takamiya, N.Terawaki, H.Kondo, N.Hayashi, F.Shimoaka, T.Matsuoka, S.Matsumori, N.Murata, M.Sonoyama, M.Sugiyama, S.

(2026) Int J Biol Macromol 369: 152710-152710

  • DOI: https://doi.org/10.1016/j.ijbiomac.2026.152710
  • Primary Citation Related Structures: 
    7FBF, 7FD7, 7FEK, 7WPG

  • PubMed Abstract: 

    PFAS are widely employed in a broad range of applications, spanning from consumer products, such as non-stick cookware, to industrial processes including semiconductor manufacturing. However, PFAS can accumulate in the human body, and certain compounds have been reported to exhibit carcinogenic potential. Perfluoroalkyl acids (PFAAs), a subclass of PFAS, have been shown to bioaccumulate via interactions with fatty acid-binding proteins (FABPs), although the molecular basis for their recognition remains incompletely elucidated. In this study, fluorescence displacement assays revealed that two perfluoroalkyl acids (PFAAs) showed lower apparent IC₅₀ values for human FABP3 than their corresponding physiological ligands, medium-chain fatty acids (MCFAs). We also determined the ultra-high resolution crystal structures of FABP3 in complex with PFAAs and with MCFAs, thereby providing a molecular basis for PFAAs recognition by FABP3. Structural comparisons demonstrated that PFAAs adopt conformations resembling MCFAs but show distinct solvent-coupled features, including close O···F contacts with ordered water molecules in the binding pocket. Our findings suggest that FABP3 recognizes PFAAs through a mechanism partially shared with fatty acids, but not fully explained by hydrophobic effects alone, with possible additional contributions from dipole-interactive effects. This work provides structural insight into PFAS recognition and suggests a molecular basis by which PFAS could interfere with fatty acid binding to FABPs.


  • Organizational Affiliation
    • Graduate School of Integrated Arts and Sciences, Kochi University, Kochi, 780-8520, Japan.

Macromolecule Content 

  • Total Structure Weight: 15.29 kDa 
  • Atom Count: 1,510 
  • Modeled Residue Count: 133 
  • Deposited Residue Count: 133 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fatty acid-binding protein, heart133Homo sapiensMutation(s): 0 
Gene Names: FABP3FABP11MDGI
UniProt & NIH Common Fund Data Resources
Find proteins for P05413 (Homo sapiens)
Explore P05413 
Go to UniProtKB:  P05413
PHAROS:  P05413
GTEx:  ENSG00000121769 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05413
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.90 Å
  • R-Value Free:  0.126 (Depositor), 0.135 (DCC) 
  • R-Value Work:  0.113 (Depositor), 0.120 (DCC) 
  • R-Value Observed: 0.114 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.588α = 90
b = 69.815β = 90
c = 33.896γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Science and TechnologyJPMJTM19DC
Japan Science and TechnologyJPMJER1005
Japan Society for the Promotion of Science (JSPS)19K06588
Other private09-003-005

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2026-06-24
    Changes: Database references, Structure summary