4TKB

The 0.86 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with lauric acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.86 Å
  • R-Value Free: 0.121 
  • R-Value Work: 0.109 
  • R-Value Observed: 0.109 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Water-mediated recognition of simple alkyl chains by heart-type Fatty-Acid-binding protein

Matsuoka, S.Sugiyama, S.Matsuoka, D.Hirose, M.Lethu, S.Ano, H.Hara, T.Ichihara, O.Kimura, S.R.Murakami, S.Ishida, H.Mizohata, E.Inoue, T.Murata, M.

(2015) Angew Chem Int Ed Engl 54: 1508-1511

  • DOI: 10.1002/anie.201409830
  • Primary Citation of Related Structures:  
    3WVM, 4TJZ, 4TKB, 4TKH, 4TKJ

  • PubMed Abstract: 
  • Long-chain fatty acids (FAs) with low water solubility require fatty-acid-binding proteins (FABPs) to transport them from cytoplasm to the mitochondria for energy production. However, the precise mechanism by which these proteins recognize the various lengths of simple alkyl chains of FAs with similar high affinity remains unknown ...

    Long-chain fatty acids (FAs) with low water solubility require fatty-acid-binding proteins (FABPs) to transport them from cytoplasm to the mitochondria for energy production. However, the precise mechanism by which these proteins recognize the various lengths of simple alkyl chains of FAs with similar high affinity remains unknown. To address this question, we employed a newly developed calorimetric method for comprehensively evaluating the affinity of FAs, sub-Angstrom X-ray crystallography to accurately determine their 3D structure, and energy calculations of the coexisting water molecules using the computer program WaterMap. Our results clearly showed that the heart-type FABP (FABP3) preferentially incorporates a U-shaped FA of C10-C18 using a lipid-compatible water cluster, and excludes longer FAs using a chain-length-limiting water cluster. These mechanisms could help us gain a general understanding of how proteins recognize diverse lipids with different chain lengths.


    Organizational Affiliation

    JST-ERATO and Graduate School of Science, Osaka University, Machikaneyama, Toyonaka, Osaka 560-0043 (Japan); Project Research Centre for Fundamental Science, Osaka University, Machikaneyama, Toyonaka, Osaka 560-0043 (Japan).



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fatty acid-binding protein, heartA133Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P6G
Query on P6G

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
DAO (Subject of Investigation/LOI)
Query on DAO

Download Ideal Coordinates CCD File 
B [auth A]LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.86 Å
  • R-Value Free: 0.121 
  • R-Value Work: 0.109 
  • R-Value Observed: 0.109 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.479α = 90
b = 69.765β = 90
c = 33.837γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPS KAKENHIJapan25286051
JSPS KAKENHIJapan25650051
JSP ERATOJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2015-02-04
    Changes: Database references
  • Version 1.2: 2020-01-29
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Source and taxonomy