7FD7

The 1.00 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with perfluoroheptanoic acid

PDB DOI: https://doi.org/10.2210/pdb7FD7/pdb

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

Deposited: 2021-07-16 Released: 2022-07-20
Deposition Author(s): Sugiyama, S., Kakinouchi, K., Hara, T., 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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free: 0.147
R-Value Work: 0.122
R-Value Observed: 0.123

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 1.00 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with perfluoroheptanoic acid

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

To be published.

Macromolecule Content

Total Structure Weight: 15.85 kDa
Atom Count: 1,590
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) Explore P05413 Go to UniProtKB: P05413
PHAROS: P05413 GTEx: ENSG00000121769
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05413
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4EI (Subject of Investigation/LOI) Query on 4EI Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	perfluoroheptanoic acid C₇ H F₁₃ O₂ ZWBAMYVPMDSJGQ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
1PE (Subject of Investigation/LOI) Query on 1PE Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free: 0.147
R-Value Work: 0.122
R-Value Observed: 0.123
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.829	α = 90
b = 69.493	β = 90
c = 33.881	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: 2022-07-20

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
Other private	Japan	09-003-005

Revision History (Full details and data files)

Version 1.0: 2022-07-20
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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7FD7

The 1.00 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with perfluoroheptanoic acid

The 1.00 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with perfluoroheptanoic acid

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)