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.

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

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

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INTESTINAL FATTY ACID BINDING PROTEIN	A	131	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P02693 (Rattus norvegicus) Explore P02693 Go to UniProtKB: P02693
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02693
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLM Query on PLM Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain B [auth A]

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 1992-01-15

Deposition Author(s):

Sacchettini, J.C.

Gordon, J.I.

Banaszak, L.J.

Revision History (Full details and data files)

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
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations, Other