3STM

Structure of human LFABP in complex with one molecule of palmitic acid

PDB DOI: https://doi.org/10.2210/pdb3STM/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-07-11 Released: 2011-08-10
Deposition Author(s): Sharma, A., Sharma, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free: 0.281
R-Value Work: 0.242
R-Value Observed: 0.243

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Fatty acid induced remodeling within the Human liver fatty acid binding protein

Sharma, A., Sharma, A.

(2011) J Biol Chem

PubMed: 21757748 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1074/jbc.M111.270165
Primary Citation of Related Structures:
3STK, 3STM, 3STN

PubMed Abstract:
We crystallized human liver fatty acid-binding protein (LFABP) in apo, holo, and intermediate states of palmitic acid engagement. Structural snapshots of fatty acid recognition, entry, and docking within LFABP support a heads-in mechanism for ligand entry. Apo-LFABP undergoes structural remodeling, where the first palmitate ingress creates the atomic environment for placement of the second palmitate. These new mechanistic insights will facilitate development of pharmacological agents against LFABP.

Organizational Affiliation

Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Road, 110067 New Delhi, India.

Macromolecule Content

Total Structure Weight: 14.86 kDa
Atom Count: 1,065
Modelled Residue Count: 127
Deposited Residue Count: 132
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acid-binding protein, liver	A [auth X]	132	Homo sapiens	Mutation(s): 0 Gene Names: FABP1, FABPL
UniProt & NIH Common Fund Data Resources
Find proteins for P07148 (Homo sapiens) Explore P07148 Go to UniProtKB: P07148
PHAROS: P07148 GTEx: ENSG00000163586
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07148
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 X] MOL2 format, chain B [auth X]	B [auth X]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free: 0.281
R-Value Work: 0.242
R-Value Observed: 0.243
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.236	α = 90
b = 57.392	β = 90
c = 74.404	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
DENZO	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-08-10

Deposition Author(s):

Sharma, A.

Revision History (Full details and data files)

Version 1.0: 2011-08-10
Type: Initial release
Version 1.1: 2017-11-08
Changes: Refinement description
Version 1.2: 2024-03-20
Changes: Data collection, Database references, Derived calculations