7WC3 | pdb_00007wc3

X-ray structure of the human adipocyte fatty acid-binding protein complexed with the fluorescent probe HA728

PDB DOI: https://doi.org/10.2210/pdb7WC3/pdb

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

Deposited: 2021-12-18 Released: 2022-12-21
Deposition Author(s): Takahashi, J., Matsuoka, S., Tsuchikawa, H., Sonoyama, M., Inoue, Y., Hayashi, F., Murata, M., Sugiyama, S.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.175 (Depositor), 0.180 (DCC)
R-Value Work:
0.123 (Depositor), 0.128 (DCC)
R-Value Observed:
0.125 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7WC3

Ligand Structure Quality Assessment

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

Literature

X-ray structure of the human adipocyte fatty acid-binding protein complexed with the fluorescent probe HA728

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

To be published.

Macromolecule Content

Total Structure Weight: 15.03 kDa
Atom Count: 1,332
Modeled Residue Count: 129
Deposited Residue Count: 132
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acid-binding protein, adipocyte	A	132	Homo sapiens	Mutation(s): 0 Gene Names: FABP4
UniProt & NIH Common Fund Data Resources
Find proteins for P15090 (Homo sapiens) Explore P15090 Go to UniProtKB: P15090
PHAROS: P15090 GTEx: ENSG00000170323
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P15090
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8QU (Subject of Investigation/LOI) Query on 8QU 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]	(3S)-1-(4-nitro-2,1,3-benzoxadiazol-7-yl)piperidine-3-carboxylic acid C₁₂ H₁₂ N₄ O₅ OUFPFDCBWRREOT-ZETCQYMHSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.175 (Depositor), 0.180 (DCC)
R-Value Work: 0.123 (Depositor), 0.128 (DCC)
R-Value Observed: 0.125 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.98	α = 90
b = 71.665	β = 90
c = 31.637	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-12-21

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2022-12-21
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.