7WKB | pdb_00007wkb

The 0.81 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with docosahexaenoic acid

• PDB DOI: https://doi.org/10.2210/pdb7WKB/pdb

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


• Deposited: 2022-01-08 Released: 2023-01-25 
• Deposition Author(s): Sugiyama, S., Kakinouchi, K., Nakano, R., Matsuoka, S., Tsuchikawa, H., Sonoyama, M., Inoue, Y., Hayashi, F., Murata, M.
• Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science (JSPS), Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.81 Å
• R-Value Free: 
  0.133 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.119 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.120 (Depositor) 

Starting Model: experimental

Literature

The 0.81 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with docosahexaenoic acid

Sugiyama, S., Kakinouchi, K., Nakano, R., Matsuoka, S., Tsuchikawa, H., Sonoyama, M., Inoue, Y., Hayashi, F., Murata, M.

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: 15.45 kDa 
• Atom Count: 1,611 
• Modelled 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): 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
HXA (Subject of Investigation/LOI)	B [auth A]	DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID C22 H32 O2 MBMBGCFOFBJSGT-KUBAVDMBSA-N
1PE (Subject of Investigation/LOI)	C [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.81 Å
• R-Value Free:  0.133 (Depositor), 0.140 (DCC) 
• R-Value Work:  0.119 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.120 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.551	α = 90
b = 69.427	β = 90
c = 33.926	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: 2023-01-25 
Deposition Author(s): Sugiyama, S., Kakinouchi, K., Nakano, R., Matsuoka, S., Tsuchikawa, H., Sonoyama, M., Inoue, Y., Hayashi, F., Murata, M.

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Funding Organization	Location	Grant Number
Japan Science and Technology		JPMJTM19DC
Japan Science and Technology		JPMJER1005
Japan Society for the Promotion of Science (JSPS)		19K06588
Other private		09-003-005

Revision History  

• Version 1.0: 2023-01-25
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description