2HMB

THREE-DIMENSIONAL STRUCTURE OF RECOMBINANT HUMAN MUSCLE FATTY ACID-BINDING PROTEIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Three-dimensional structure of recombinant human muscle fatty acid-binding protein.

Zanotti, G.Scapin, G.Spadon, P.Veerkamp, J.H.Sacchettini, J.C.

(1992) J Biol Chem 267: 18541-18550

  • DOI: https://doi.org/10.2210/pdb2hmb/pdb
  • Primary Citation of Related Structures:  
    2HMB

  • PubMed Abstract: 

    The three-dimensional structure of recombinant human muscle fatty acid-binding protein with a bound fatty acid has been solved and refined with x-ray diffraction data to 2.1 A resolution. The refined model has a crystallographic R factor of 19.5% for data between 9.0 and 2.1 A (7243 unique reflections) and root-mean-square deviations in bond length and bond angle of 0.013 A and 2.7 degrees. The protein contains 10 antiparallel beta-strands and two short alpha-helices which are arranged into two approximately orthogonal beta-sheets. Difference electron density maps and a multiple isomorphous derivative electron density map showed the presence of a single bound molecule of a long chain fatty acid within the interior core of the protein. The hydrocarbon tail of the fatty acid was found to be in a "U-shaped" conformation. Seven ordered water molecules were also identified within the interior of the protein in a pocket on the pseudo-si face of the fatty acid's bent hydrocarbon tail. The methylene tail of the fatty acid forms van der Waals interactions with atoms from 13 residues and three ordered waters. The carboxylate of the fatty acid is located in the interior of the protein where it forms hydrogen bonds with the side chains of Tyr128 and Arg126 and two ordered water molecules. A comparison of the three-dimensional structure of human muscle fatty acid-binding protein and rat intestinal fatty acid-binding protein shows strong similarity. Both proteins bind a single fatty acid within their interior cores, but the bound fatty acids are very different in their conformations and interactions. These findings suggest that the intestinal and muscle fatty acid-binding proteins have evolved distinct binding sites in order to satisfy different requirements within the tissues where they are expressed.


  • Organizational Affiliation

    Department of Organic Chemistry, University of Padova, Italy.


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
PLM
Query on PLM

Download Ideal Coordinates CCD File 
B [auth A]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
PLM PDBBind:  2HMB IC50: 2600 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.4α = 90
b = 56.7β = 90
c = 72.7γ = 90
Software Package:
Software NamePurpose
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: 1994-01-31
    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: Derived calculations, Other, Structure summary
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations