7X48

The 0.86 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with pelargonic acid

PDB DOI: https://doi.org/10.2210/pdb7X48/pdb

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

Deposited: 2022-03-02 Released: 2023-03-08
Deposition Author(s): Sugiyama, S., 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.86 Å
R-Value Free: 0.127
R-Value Work: 0.112
R-Value Observed: 0.113

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The 0.86 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with pelargonic acid

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

To be published.

Macromolecule Content

Total Structure Weight: 15.32 kDa
Atom Count: 1,578
Modelled Residue Count: 133
Deposited Residue Count: 133
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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) Go to UniProtKB: P05413
PHAROS: P05413 GTEx: ENSG00000121769
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G (Subject of Investigation/LOI) Query on P6G Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain C [auth A]
KNA (Subject of Investigation/LOI) Query on KNA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	nonanoic acid C₉ H₁₈ O₂ FBUKVWPVBMHYJY-UHFFFAOYSA-N		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.86 Å
R-Value Free: 0.127
R-Value Work: 0.112
R-Value Observed: 0.113
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.584	α = 90
b = 69.875	β = 90
c = 33.858	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-03-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJTM19DC
Japan Society for the Promotion of Science (JSPS)	Japan	19K06588
Japan Science and Technology	Japan	JPMJER1005

Revision History (Full details and data files)

Version 1.0: 2023-03-08
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.