4WBK

The 1.37 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with stearic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Molecular Dynamics Simulations of Heart-type Fatty Acid Binding Protein in Apo and Holo Forms, and Hydration Structure Analyses in the Binding Cavity

Matsuoka, D.Sugiyama, S.Murata, M.Matsuoka, S.

(2015) J.Phys.Chem.B 119: 114-127

  • DOI: 10.1021/jp510384f

  • PubMed Abstract: 
  • Intracellular lipid binding proteins (iLBPs) share distinctive features: a rigid protein structure composed of a β-barrel and an α-helix cap, and a large internalized water cluster. Although X-ray crystallographic studies have elucidated the three-di ...

    Intracellular lipid binding proteins (iLBPs) share distinctive features: a rigid protein structure composed of a β-barrel and an α-helix cap, and a large internalized water cluster. Although X-ray crystallographic studies have elucidated the three-dimensional structures of iLBPs, the protein dynamics and the role of the large water cluster in protein function remain unknown. In the present study, we performed molecular dynamics (MD) simulations on human heart-type fatty acid binding protein (FABP3), a typical iLBP that is highly expressed in heart and skeletal muscles, and showed that an altered mode of protein dynamics and rearrangement of the internal water cluster are key elements of ligand binding. Using simulations without a ligand at 310 K, we first demonstrated that FABP3 adopts a wide-open conformation, achieved by a combination of two modes of dynamics: portal opening by a domain motion of the α-helices and gap opening by cleavage of the hydrogen-bond network between βD and βE strands. In contrast, stearic acid-bound FABP3 mainly adopted a closed form, stabilized by the H-bond network inside the binding cavity, which latches the gap, and by protein-ligand hydrophobic interactions. The wide-open apo FABP3 represents a biologically important conformation relevant to ligand loading.


    Organizational Affiliation

    JST ERATO, Lipid Active Structure Project, ‡Department of Chemistry, Graduate School of Science, and §Project Research Center for Fundamental Science, Osaka University , 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fatty acid-binding protein, heart
A
133Homo sapiensMutation(s): 0 
Gene Names: FABP3 (FABP11, MDGI)
Find proteins for P05413 (Homo sapiens)
Go to Gene View: FABP3
Go to UniProtKB:  P05413
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
STE
Query on STE

Download SDF File 
Download CCD File 
A
STEARIC ACID
C18 H36 O2
QIQXTHQIDYTFRH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.153 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.645α = 90.00
b = 68.807β = 90.00
c = 33.620γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPS KAKENHIJapan25286051

Revision History 

  • Version 1.0: 2015-01-28
    Type: Initial release