2IFB

CRYSTAL STRUCTURE OF RAT INTESTINAL FATTY-ACID-BINDING PROTEIN. REFINEMENT AND ANALYSIS OF THE ESCHERICHIA COLI-DRIVED PROTEIN WITH BOUND PALMITATE

• PDB DOI:  https://doi.org/10.2210/pdb2IFB/pdb

• Classification: FATTY ACID-BINDING PROTEIN
• Organism(s): Rattus norvegicus
• Mutation(s): No 


• Deposited: 1990-12-05 Released: 1992-01-15 
• Deposition Author(s): Sacchettini, J.C., Gordon, J.I., Banaszak, L.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.178 

Literature

Crystal structure of rat intestinal fatty-acid-binding protein. Refinement and analysis of the Escherichia coli-derived protein with bound palmitate.

Sacchettini, J.C., Gordon, J.I., Banaszak, L.J.

(1989) J Mol Biol 208: 327-339

• PubMed: 2671390 
• DOI: https://doi.org/10.1016/0022-2836(89)90392-6
• Primary Citation of Related Structures:  
  2IFB


• PubMed Abstract: 
  

Rat intestinal fatty-acid-binding protein (I-FABP) is a small (15,124 Mr) cytoplasmic polypeptide that binds long-chain fatty acids in a non-covalent fashion. I-FABP is a member of a family of intracellular binding proteins that are thought to participate in the uptake, transport and/or metabolic targeting of hydrophobic ligands. The crystal structure of Escherichia coli-derived rat I-FABP with a single molecule of bound palmitate has been refined to 2 A resolution using a combination of least-squares methods, energy refinement and molecular dynamics. The combined methods resulted in a model with a crystallographic R-factor of 17.8% (7775 reflections, sigma greater than 2.0), root-mean-square bond length deviation of 0.009 A and root-mean-square bond angle deviation of 2.85 degrees. I-FABP contains ten antiparallel beta-strands organized into two approximately orthogonal, beta-sheets. The hydrocarbon tail of its single C16:0 ligand is present in a well-ordered, distinctively bent conformation. The carboxylate group of the fatty acid is located in the interior of I-FABP and forms a unique "quintet" of electrostatic interactions involving Arg106; Gln 115, and two solvent molecules. The hydrocarbon tail is bent with a slight left-handed helical twist from the carboxylate group to C-16. The bent methylene chain resides in a "cradle" formed by the side-chains of hydrophobic, mainly aromatic, amino acid residues. The refined molecular model of holo-I-FABP suggests several potential locations for entry and exiting of the fatty acid.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO 63110.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.27 kDa 
• Atom Count: 1,136 
• Modelled Residue Count: 131 
• Deposited Residue Count: 131 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INTESTINAL FATTY ACID BINDING PROTEIN	A	131	Rattus norvegicus	Mutation(s): 0  Gene Names: Fabp2, Fabpi
UniProt
Find proteins for P02693 (Rattus norvegicus) Explore P02693  Go to UniProtKB:  P02693

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLM	B [auth A]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
PLM	Binding MOAD:  2IFB	Ki: 3600 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.178 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.8	α = 90
b = 56.9	β = 114
c = 31.9	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1992-01-15 
Deposition Author(s): Sacchettini, J.C., Gordon, J.I., Banaszak, L.J.

Revision History  

• Version 1.0: 1992-01-15
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance