7G1M

Crystal Structure of human FABP4 binding site mutated to that of FABP5 in complex with rac-(1R,2R)-2-[[3-(3-methyl-1,2,4-oxadiazol-5-yl)-4,5,6,7-tetrahydro-1-benzothiophen-2-yl]carbamoyl]cyclohexane-1-carboxylic acid

PDB DOI: https://doi.org/10.2210/pdb7G1M/pdb
Deposition Group: G_1002264 ExploreG_1002264

Classification: LIPID BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-04-27 Released: 2023-06-14
Deposition Author(s): Ehler, A., Benz, J., Obst, U., Neidhart, W., Rudolph, M.G.
Funding Organization(s): F. Hoffmann-La Roche LTD

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.34 Å
R-Value Free: 0.198
R-Value Work: 0.151
R-Value Observed: 0.154

Starting Model: other
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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

Crystal Structure of a human FABP4 binding site mutated to that of FABP5 complex

Obst, U., Magnone, C., Kuhn, B., Rudolph, M.G.

To be published.

Macromolecule Content

Total Structure Weight: 15.4 kDa
Atom Count: 1,220
Modelled Residue Count: 130
Deposited Residue Count: 135
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acid-binding protein, adipocyte	A	135	Homo sapiens	Mutation(s): 8 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15090
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WOU (Subject of Investigation/LOI) Query on WOU 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]	(1R,2S)-2-{[(3M)-3-(3-methyl-1,2,4-oxadiazol-5-yl)-4,5,6,7-tetrahydro-1-benzothiophen-2-yl]carbamoyl}cyclohexane-1-carboxylic acid C₁₉ H₂₃ N₃ O₄ S DNXAITYNLMDHGE-NWDGAFQWSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.34 Å
R-Value Free: 0.198
R-Value Work: 0.151
R-Value Observed: 0.154
Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.015	α = 90
b = 52.942	β = 90
c = 72.164	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-06-14

Deposition Author(s):

Funding Organization	Location	Grant Number
F. Hoffmann-La Roche LTD	Switzerland	--

Revision History (Full details and data files)

Version 1.0: 2023-06-14
Type: Initial release
Version 1.1: 2024-04-03
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.