8G4A | pdb_00008g4a

Human ARNT PAS-B complexed with KG-548 small molecule

PDB DOI: https://doi.org/10.2210/pdb8G4A/pdb

Classification: TRANSCRIPTION/INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-02-08 Released: 2024-02-14
Deposition Author(s): Xu, X., Isiorho, E.A., Pimentel Marcelino, L., Gardner, K.H.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free:
0.229 (Depositor), 0.230 (DCC)
R-Value Work:
0.204 (Depositor), 0.210 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Use of High Pressure NMR Spectroscopy to Rapidly Identify Proteins with Internal Ligand-Binding Voids

Gagne, D., Azad, R., Aramini, J.M., Xu, X., Isiorho, E.A., Edupuganti, U.R., Williams, J., Marcelino, L.P., Akasaka, K., Gardner, K.H.

(2023) bioRxiv

DOI: https://doi.org/10.1101/2020.08.25.267195

Macromolecule Content

Total Structure Weight: 28.2 kDa
Atom Count: 1,787
Modeled Residue Count: 211
Deposited Residue Count: 238
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aryl hydrocarbon receptor nuclear translocator	A, B	119	Homo sapiens	Mutation(s): 0 Gene Names: ARNT, BHLHE2
UniProt & NIH Common Fund Data Resources
Find proteins for P27540 (Homo sapiens) Explore P27540 Go to UniProtKB: P27540
PHAROS: P27540 GTEx: ENSG00000143437
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P27540
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YL8 (Subject of Investigation/LOI) Query on YL8 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]	5-[3,5-bis(trifluoromethyl)phenyl]-2H-tetrazole C₉ H₄ F₆ N₄ KKJFZIQEWZVVIV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.229 (Depositor), 0.230 (DCC)
R-Value Work: 0.204 (Depositor), 0.210 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.135	α = 90
b = 80.135	β = 90
c = 100.718	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Blu-Ice	data collection
autoPROC	data reduction
PHASER	phasing
PDB-REDO	refinement
autoPROC	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-02-14

Deposition Author(s):

Pimentel Marcelino, L.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB1818148

Revision History (Full details and data files)

Version 1.0: 2024-02-14
Type: Initial release
Version 1.1: 2025-08-27
Changes: Database references, Structure summary

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.