6X37 | pdb_00006x37

Crystal structure of PT3245 bound to HIF2a-B*:ARNT-B* complex

• PDB DOI: https://doi.org/10.2210/pdb6X37/pdb

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


• Deposited: 2020-05-21 Released: 2021-05-26 
• Deposition Author(s): Du, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.282 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of PT3245 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: 27.53 kDa 
• Atom Count: 1,848 
• Modeled Residue Count: 218 
• 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
ULS (Subject of Investigation/LOI)	C [auth A]	3-fluoro-5-{[(7R)-7-hydroxy-1-(trifluoromethyl)-6,7-dihydro-5H-cyclopenta[c]pyridin-4-yl]oxy}benzonitrile C16 H10 F4 N2 O2 QJVMUDSPENWIOV-GFCCVEGCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.282 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.298	α = 90
b = 83.974	β = 106.31
c = 41.433	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
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