1HMR

1.4 ANGSTROMS STRUCTURAL STUDIES ON HUMAN MUSCLE FATTY ACID BINDING PROTEIN: BINDING INTERACTIONS WITH THREE SATURATED AND UNSATURATED C18 FATTY ACIDS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Work: 0.132 
  • R-Value Observed: 0.132 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Structural studies on human muscle fatty acid binding protein at 1.4 A resolution: binding interactions with three C18 fatty acids.

Young, A.C.Scapin, G.Kromminga, A.Patel, S.B.Veerkamp, J.H.Sacchettini, J.C.

(1994) Structure 2: 523-534

  • DOI: https://doi.org/10.1016/s0969-2126(00)00052-6
  • Primary Citation of Related Structures:  
    1HMR, 1HMS, 1HMT

  • PubMed Abstract: 

    Muscle fatty acid binding protein (M-FABP) is one of a family of cytosolic lipid-binding proteins involved in fatty acid processing. In order to investigate the precise interactions between M-FABP and its ligands and to understand the structural basis of differential binding affinity, we have compared the structures of M-FABP in complex with three C18 fatty acids. We describe the crystal structures of M-FABP in complex with n-octadecanoate (stearate), trans-delta 9-octadecenoate (elaidate) and cis-delta 9-octadecenoate (oleate). These structures were refined using least-squares positional and anisotropic temperature factor refinement to final R-factors of 11.4%, 12.1% and 13.2% respectively for all the data between 8.0 A and 1.4 A resolution. Stearate, elaidate and oleate each adopt highly similar U-shaped conformations when they bind to M-FABP within a large interior binding cavity, which also contains 13 ordered water molecules. The atomic structure of the protein is virtually identical, regardless of the nature of the bound ligand. The fatty acid is thought to enter the interior cavity of the protein via a portal in its surface while interior solvent is released through a secondary opening. The ligand affinity can be correlated with the conformational energy and the solubility of the bound ligand.


  • Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MUSCLE FATTY ACID BINDING PROTEIN132Homo sapiensMutation(s): 0 
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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ELA
Query on ELA

Download Ideal Coordinates CCD File 
B [auth A]9-OCTADECENOIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-MDZDMXLPSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
ELA PDBBind:  1HMR Kd: 280 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Work: 0.132 
  • R-Value Observed: 0.132 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.65α = 90
b = 55.42β = 90
c = 71.31γ = 90
Software Package:
Software NamePurpose
SHELXLrefinement
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-05-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Structure summary
  • Version 1.4: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.5: 2019-08-14
    Changes: Data collection, Refinement description
  • Version 1.6: 2024-02-07
    Changes: Data collection, Database references, Derived calculations