6X21 | pdb_00006x21

Crystal structure of PT1673 bound to HIF2a-B*:ARNT-B* complex

• PDB DOI: https://doi.org/10.2210/pdb6X21/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-05-19 Released: 2021-05-26 
• Deposition Author(s): Du, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of PT1673 bound to HIF2a-B*:ARNT-B* complex

Du, X.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 27.62 kDa 
• Atom Count: 1,881 
• Modeled Residue Count: 214 
• Deposited Residue Count: 233 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endothelial PAS domain-containing protein 1	A	115	Homo sapiens	Mutation(s): 1  Gene Names: EPAS1, BHLHE73, HIF2A, MOP2, PASD2
UniProt & NIH Common Fund Data Resources
Find proteins for Q99814 (Homo sapiens) Explore Q99814  Go to UniProtKB:  Q99814
PHAROS:  Q99814 GTEx:  ENSG00000116016

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aryl hydrocarbon receptor nuclear translocator	B	118	Homo sapiens	Mutation(s): 1  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UKJ (Subject of Investigation/LOI)	C [auth A]	1-(3-bromo-5-fluorophenoxy)-4-[(difluoromethyl)sulfonyl]-2-nitrobenzene C13 H7 Br F3 N O5 S DRYZYPGPBXQGKZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free:  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.793	α = 90
b = 83.504	β = 106.78
c = 41.373	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-05-26 
Deposition Author(s): Du, X.

Revision History  

• Version 1.0: 2021-05-26
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description