2HNX

Crystal Structure of aP2

• PDB DOI: https://doi.org/10.2210/pdb2HNX/pdb

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


• Deposited: 2006-07-13 Released: 2006-11-28 
• Deposition Author(s): Marr, E., Tardie, M., Carty, M., Brown Phillips, T., Qiu, X., Karam, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.225 
• R-Value Work: 0.174 
• R-Value Observed: 0.177 

Literature

Expression, purification, crystallization and structure of human adipocyte lipid-binding protein (aP2).

Marr, E., Tardie, M., Carty, M., Brown Phillips, T., Wang, I.K., Soeller, W., Qiu, X., Karam, G.

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 1058-1060

• PubMed: 17077479 
• DOI: https://doi.org/10.1107/S1744309106038656
• Primary Citation of Related Structures:  
  2HNX


• PubMed Abstract: 
  

  Human adipocyte lipid-binding protein (aP2) belongs to a family of intracellular lipid-binding proteins involved in the transport and storage of lipids. Here, the crystal structure of human aP2 with a bound palmitate is described at 1.5 A resolution. Unlike the known crystal structure of murine aP2 in complex with palmitate, this structure shows that the fatty acid is in a folded conformation and that the loop containing Phe57 acts as a lid to regulate ligand binding by excluding solvent exposure to the central binding cavity.

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Organizational Affiliation: 

Exploratory Medicinal Sciences, Pfizer Global Research and Development Groton Laboratories, Eastern Point Road, Groton, CT 06340, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.65 kDa 
• Atom Count: 1,300 
• Modelled Residue Count: 136 
• Deposited Residue Count: 136 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acid-binding protein, adipocyte	A	136	Homo sapiens	Mutation(s): 0  Gene Names: FABP4
UniProt & NIH Common Fund Data Resources
Find proteins for P15090 (Homo sapiens) Explore P15090  Go to UniProtKB:  P15090
PHAROS:  P15090 GTEx:  ENSG00000170323

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLM	C [auth A]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ACY	D [auth A], E [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
PLM	PDBBind:  2HNX	Kd: 83 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.225 
• R-Value Work: 0.174 
• R-Value Observed: 0.177 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.47	α = 90
b = 53.94	β = 90
c = 75	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-28 
Deposition Author(s): Marr, E., Tardie, M., Carty, M., Brown Phillips, T., Qiu, X., Karam, G.

Revision History  

• Version 1.0: 2006-11-28
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations