3AKM | pdb_00003akm

X-ray structure of iFABP from human and rat with bound fluorescent fatty acid analogue

• PDB DOI: https://doi.org/10.2210/pdb3AKM/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2010-07-14 Released: 2011-07-20 
• Deposition Author(s): Wielens, J., Laguerre, A.J.K., Parker, M.W., Scanlon, M.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.279 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of human and rat intestinal fatty acid binding proteins in complex with 11-(Dansylamino)undecanoic acid

Laguerre, A.J.K., Wielens, J., Parker, M.W., Porter, C.J., Scanlon, M.J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 62.23 kDa 
• Atom Count: 4,463 
• Modeled Residue Count: 524 
• Deposited Residue Count: 524 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acid-binding protein, intestinal	A, B, C, D	131	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P12104 (Homo sapiens) Explore P12104  Go to UniProtKB:  P12104
PHAROS:  P12104 GTEx:  ENSG00000145384

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
11D	E [auth A], G [auth B], I [auth C], K [auth D]	11-({[5-(dimethylamino)naphthalen-1-yl]sulfonyl}amino)undecanoic acid C23 H34 N2 O4 S CEPGVMDMVJGHFQ-UHFFFAOYSA-N
MG	F [auth A], H [auth B], J [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
11D	BindingDB:  3AKM	Ki: 300 (nM) from 1 assay(s)
		Kd: 360 (nM) from 1 assay(s)
		-TΔS: 9.96 (kJ/mol) from 1 assay(s)
		ΔH: -4.81e+1 (kJ/mol) from 1 assay(s)
		ΔG: -3.83e+1 (kJ/mol) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.279 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.02	α = 90
b = 79.011	β = 94.48
c = 63.24	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-20 
Deposition Author(s): Wielens, J., Laguerre, A.J.K., Parker, M.W., Scanlon, M.J.

Revision History  

• Version 1.0: 2011-07-20
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description