7EGO | pdb_00007ego

X-ray structure of the human heart fatty acid-binding protein complexed with the fluorescent probe HA527

• PDB DOI: https://doi.org/10.2210/pdb7EGO/pdb

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


• Deposited: 2021-03-24 Released: 2022-03-30 
• Deposition Author(s): Takabayashi, M., Yokota, J., Matsuoka, S., Tsuchikawa, H., Sonoyama, M., Inoue, Y., Hayashi, F., Sugiyama, S.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology, Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free: 
  0.152 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.129 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.130 (Depositor) 

Starting Model: experimental

Literature

X-ray structure of the human heart fatty acid-binding protein complexed with the fluorescent probe HA527

Matsuoka, S., Tsuchikawa, H., Sonoyama, M., Inoue, Y., Hayashi, F., Sugiyama, S.

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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 15.71 kDa 
• Atom Count: 1,386 
• Modeled Residue Count: 132 
• 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): 0  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
P6G (Subject of Investigation/LOI)	C [auth A], D [auth A]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
J3R (Subject of Investigation/LOI)	B [auth A]	3-[methyl-(4-nitro-2,1,3-benzoxadiazol-7-yl)amino]propanoic acid C10 H10 N4 O5 SPMMNZGTRNFEDD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free:  0.152 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.129 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.130 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.521	α = 90
b = 69.657	β = 90
c = 33.844	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-03-30 
Deposition Author(s): Takabayashi, M., Yokota, J., Matsuoka, S., Tsuchikawa, H., Sonoyama, M., Inoue, Y., Hayashi, F., Sugiyama, S.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	19K06588
Japan Science and Technology	Japan	JPMJTM19DC
Other private	Japan	09-003-005

Revision History  

• Version 1.0: 2022-03-30
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description