5B28 | pdb_00005b28

The 0.90A structure of human FABP3 F16V mutant complexed with palmitic acid

• PDB DOI: https://doi.org/10.2210/pdb5B28/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-01-12 Released: 2017-01-18 
• Deposition Author(s): Matsuoka, D., Sugiyama, S., Kakinouchi, K., Niiyama, M., Murata, M., Matsuoka, S.
• Funding Organization(s): JSPS KAKENHI

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.90 Å
• R-Value Free: 
  0.126 (Depositor), 0.130 (DCC) 
• R-Value Work: 
  0.113 (Depositor), 0.115 (DCC) 
• R-Value Observed: 
  0.113 (Depositor) 

Starting Model: experimental

Literature

The 0.90A structure of human FABP3 F16V mutant complexed with palmitic acid.

Matsuoka, D., Sugiyama, S., Kakinouchi, K., Niiyama, M., Murata, M., Matsuoka, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 15.33 kDa 
• Atom Count: 1,587 
• Modeled Residue Count: 133 
• Deposited Residue Count: 133 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acid-binding protein, heart	A	133	Homo sapiens	Mutation(s): 1  Gene Names: FABP3, FABP11, MDGI
UniProt & NIH Common Fund Data Resources
Find proteins for P05413 (Homo sapiens) Explore P05413  Go to UniProtKB:  P05413
PHAROS:  P05413 GTEx:  ENSG00000121769

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLM	B [auth A]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
1PE	C [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.90 Å
• R-Value Free:  0.126 (Depositor), 0.130 (DCC) 
• R-Value Work:  0.113 (Depositor), 0.115 (DCC) 
• R-Value Observed: 0.113 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.555	α = 90
b = 70.094	β = 90
c = 33.785	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-01-18 
Deposition Author(s): Matsuoka, D., Sugiyama, S., Kakinouchi, K., Niiyama, M., Murata, M., Matsuoka, S.

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Funding Organization	Location	Grant Number
JSPS KAKENHI	Japan	24681045
JSPS KAKENHI	Japan	26560436
JSPS KAKENHI	Japan	25650051
JSPS KAKENHI	Japan	25286051

Revision History  

• Version 1.0: 2017-01-18
  Type: Initial release
  
• Version 1.1: 2020-02-26
  Changes: Data collection
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description