4zph

Crystal Structure of the Heterodimeric HIF-2a:ARNT Complex with Proflavine

Method: X-RAY DIFFRACTION D_max: 131.7 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Aryl hydrocarbon receptor nuclear translocator

Mus musculus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 82–464	Fragment：UNP residues 82-464	Endothelial PAS domain-containing protein 1 × 1 （P97481） PRL PROFLAVIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；2% Tacsimate, pH 7.0, 6% PEG3350	Resolution 2.80 Å R-free 0.221
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 82–464	Fragment：UNP residues 82-464	Endothelial PAS domain-containing protein 1 × 1 （P97481）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；2% Tacsimate, pH 7.0, 6% PEG3350	Resolution 2.80 Å R-free 0.221

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 4ZPH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4ZP4 Crystal Structure of the Heterodimeric HIF-2a:ARNT Complex Deposited 2015-05-07	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 82–464（383 aa） Fragment：UNP residues 82-464	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；2% Tacsimate, pH 7.0, 6% PEG3350	Resolution 2.35 Å R-free 0.232
4ZP4 Crystal Structure of the Heterodimeric HIF-2a:ARNT Complex Deposited 2015-05-07	Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 82–464（383 aa） Fragment：UNP residues 82-464	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；2% Tacsimate, pH 7.0, 6% PEG3350	Resolution 2.35 Å R-free 0.232
4ZPK Crystal Structure of the Heterodimeric HIF-2a:ARNT Complex with HRE DNA Deposited 2015-05-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 82–464（383 aa） Fragment：UNP residues 82-464	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；289 K；4% Tacsimate, pH 6.0, 10% PEG3350	Resolution 3.60 Å R-free 0.321
4ZPR Crystal Structure of the Heterodimeric HIF-1a:ARNT Complex with HRE DNA Deposited 2015-05-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 82–464（383 aa） Fragment：UNP residues 82-464	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；100 mM MES, pH 6.0, 100 mM calcium acetate, 15% PEG400	Resolution 3.90 Å R-free 0.341
4ZQD Crystal Structure of the Heterodimeric HIF-2a:ARNT Complex with the Benzoxadiazole Antagonist 0X3 Deposited 2015-05-09	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 82–464（383 aa） Fragment：UNP residues 82-464	Not recorded	0X3 N-(3-chloro-5-fluorophenyl)-4-nitro-2,1,3-benzoxadiazol-5-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；2% Tacsimate, pH 7.0, 6% PEG3350	Resolution 2.87 Å R-free 0.254
4ZQD Crystal Structure of the Heterodimeric HIF-2a:ARNT Complex with the Benzoxadiazole Antagonist 0X3 Deposited 2015-05-09	Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 82–464（383 aa） Fragment：UNP residues 82-464	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；2% Tacsimate, pH 7.0, 6% PEG3350	Resolution 2.87 Å R-free 0.254
5NJ8 Structural basis for aryl hydrocarbon receptor mediated gene activation Deposited 2017-03-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 85–345（261 aa）	Mutation：C256S	ER3 ERBIUM (III) ION × 7 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；277 K；10 mM HEPES/NaOH pH 6.8, 18% PEG3350, 200 mM ammonium formate	Resolution 3.30 Å R-free 0.333
5NJ8 Structural basis for aryl hydrocarbon receptor mediated gene activation Deposited 2017-03-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain D 85–345（261 aa）	Mutation：C256S	ER3 ERBIUM (III) ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；277 K；10 mM HEPES/NaOH pH 6.8, 18% PEG3350, 200 mM ammonium formate	Resolution 3.30 Å R-free 0.333
5SY5 Crystal Structure of the Heterodimeric NPAS1-ARNT Complex Deposited 2016-08-10	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 82–464（383 aa） Fragment：unp residues 82-464	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；2% Tacsimate pH 7.0, 3% PEG3350	Resolution 3.20 Å R-free 0.247
5SY5 Crystal Structure of the Heterodimeric NPAS1-ARNT Complex Deposited 2016-08-10	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 82–464（383 aa） Fragment：unp residues 82-464	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；2% Tacsimate pH 7.0, 3% PEG3350	Resolution 3.20 Å R-free 0.247
5SY5 Crystal Structure of the Heterodimeric NPAS1-ARNT Complex Deposited 2016-08-10	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 82–464（383 aa） Fragment：unp residues 82-464	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；2% Tacsimate pH 7.0, 3% PEG3350	Resolution 3.20 Å R-free 0.247
5SY5 Crystal Structure of the Heterodimeric NPAS1-ARNT Complex Deposited 2016-08-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 82–464（383 aa） Fragment：unp residues 82-464 Chain C 82–464（383 aa） Fragment：unp residues 82-464 Chain E 82–464（383 aa） Fragment：unp residues 82-464	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；2% Tacsimate pH 7.0, 3% PEG3350	Resolution 3.20 Å R-free 0.247
5SY7 Crystal Structure of the Heterodimeric NPAS3-ARNT Complex with HRE DNA Deposited 2016-08-10	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 82–464（383 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；289 K；100 mM NH4F, 9% PEG 3350	Resolution 4.20 Å R-free 0.361
6E3S Crystal Structure of the Heterodimeric HIF-2 Complex with Antagonist PT2385 Deposited 2018-07-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 82–464（383 aa）	Not recorded	79A 3-{[(1S)-2,2-difluoro-1-hydroxy-7-(methylsulfonyl)-2,3-dihydro-1H-inden-4-yl]oxy}-5-fluorobenzonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；2% TACSIMATE, PH 7.0, 6% PEG3350	Resolution 3.00 Å R-free 0.249
6E3T Crystal Structure of the Heterodimeric HIF-2 Complex with Antagonist T1001 Deposited 2018-07-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 82–464（383 aa）	Not recorded	HO7 (6S)-6-(4-bromophenyl)-2,3,5,6-tetrahydroimidazo[2,1-b][1,3]thiazole × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；2% TACSIMATE, PH 7.0, 6% PEG3350	Resolution 3.00 Å R-free 0.306
6E3U Crystal Structure of the Heterodimeric HIF-2 Complex with Agonist M1001 Deposited 2018-07-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 82–464（383 aa）	Not recorded	HNJ 3-{[2-(pyrrolidin-1-yl)phenyl]amino}-1H-1lambda~6~,2-benzothiazole-1,1-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2% TACSIMATE, PH 7.0, 6% PEG3350	Resolution 2.85 Å R-free 0.258
7V7L Crystal Structure of the Heterodimeric HIF-3a:ARNT Complex Deposited 2021-08-21	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 82–464（383 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；Sodium citrate tribasic dihydrate, 2-Propanol, PEG 4000	Resolution 2.30 Å R-free 0.245
7V7W Crystal Structure of the Heterodimeric HIF-3a:ARNT Complex with oleoylethanolamide (OEA) Deposited 2021-08-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 82–464（383 aa） Fragment：Hydrocarbon receptor nuclear translocator ARNT	Not recorded	5YM (Z)-N-(2-hydroxyethyl)octadec-9-enamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；Sodium citrate tribasic dihydrate, 2-Propanol, PEG 4000	Resolution 2.51 Å R-free 0.260
7VNI AHR-ARNT PAS-B heterodimer Deposited 2021-10-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 358–466（109 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium arsenate (pH 6.5), 0.2 M MgCl2, 2 M (NH4)2SO4	Resolution 2.00 Å R-free 0.219
7VNI AHR-ARNT PAS-B heterodimer Deposited 2021-10-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 358–466（109 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium arsenate (pH 6.5), 0.2 M MgCl2, 2 M (NH4)2SO4	Resolution 2.00 Å R-free 0.219
7W80 Crystal Structure of the Heterodimeric HIF-2 in Complex with Antagonist Belzutifan Deposited 2021-12-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 82–464（383 aa）	Not recorded	72Q 3-{[(1S,2S,3R)-2,3-difluoro-1-hydroxy-7-(methylsulfonyl)-2,3-dihydro-1H-inden-4-yl]oxy}-5-fluorobenzonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；Tacsimate, PEG3350	Resolution 2.75 Å R-free 0.274
7XHV Crystal Structure of the NPAS4-ARNT heterodimer in complex with DNA Deposited 2022-04-10	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 82–360（279 aa） Fragment：ARNT	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；289 K；ammonium tartrate dibasic, PEG3350	Resolution 4.00 Å R-free 0.331
7XI4 Crystal Structure of the NPAS4-ARNT heterodimer in complex with DNA Deposited 2022-04-12	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 82–464（383 aa） Fragment：ARNT	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；289 K；ammonium tartrate dibasic, PEG3350	Resolution 4.71 Å R-free 0.351
9LJX Crystal Structure of the Heterodimeric HIF-2 Complex with Agonist SD-26 Deposited 2025-01-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 82–464（383 aa）	Not recorded	A1EKB 4-fluoranyl-~{N}-(3-fluoranyl-2-pyrrolidin-1-yl-phenyl)-1,1-bis(oxidanylidene)-1,2-benzothiazol-3-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；PEG 3350, Succinic Acid pH 7.0	Resolution 2.80 Å R-free 0.268
9LJY Crystal Structure of the Heterodimeric HIF-2 Complex with Agonist SD-14 Deposited 2025-01-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 82–464（383 aa）	Not recorded	A1EJ9 4-chloranyl-1,1-bis(oxidanylidene)-~{N}-(2-pyrrolidin-1-ylphenyl)-1,2-benzothiazol-3-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；PEG 3350, Succinic Acid pH 7.0	Resolution 3.20 Å R-free 0.248
9LOH Crystal Structure of the Heterodimeric HIF-2 Complex with Agonist SD-10 Deposited 2025-01-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 82–464（383 aa）	Not recorded	A1EJ8 4-fluoranyl-1,1-bis(oxidanylidene)-~{N}-(2-pyrrolidin-1-ylphenyl)-1,2-benzothiazol-3-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；PEG 3350, Succinic Acid pH 7.0	Resolution 3.02 Å R-free 0.262
9LOI Crystal Structure of the Heterodimeric HIF-2 Complex with Agonist SD-16 Deposited 2025-01-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 82–464（383 aa）	Not recorded	A1EKA 6-chloranyl-1,1-bis(oxidanylidene)-~{N}-(2-pyrrolidin-1-ylphenyl)-1,2-benzothiazol-3-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；PEG 3350, Succinic Acid pH 7.0	Resolution 2.78 Å R-free 0.275

20 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ARNT_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–384； UniProt 82–464 Author chain C； PDBConstruct 2–384； UniProt 82–464

Endothelial PAS domain-containing protein 1

Mus musculus

UniProt P97481

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 3–361	Fragment：UNP residues 3-361	Aryl hydrocarbon receptor nuclear translocator × 1 （P53762） PRL PROFLAVIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；2% Tacsimate, pH 7.0, 6% PEG3350	Resolution 2.80 Å R-free 0.221
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 3–361	Fragment：UNP residues 3-361	Aryl hydrocarbon receptor nuclear translocator × 1 （P53762）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；2% Tacsimate, pH 7.0, 6% PEG3350	Resolution 2.80 Å R-free 0.221

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 4ZPH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4ZP4 Crystal Structure of the Heterodimeric HIF-2a:ARNT Complex Deposited 2015-05-07	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 3–361（359 aa） Fragment：UNP residues 3-361	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；2% Tacsimate, pH 7.0, 6% PEG3350	Resolution 2.35 Å R-free 0.232
4ZP4 Crystal Structure of the Heterodimeric HIF-2a:ARNT Complex Deposited 2015-05-07	Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 3–361（359 aa） Fragment：UNP residues 3-361	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；2% Tacsimate, pH 7.0, 6% PEG3350	Resolution 2.35 Å R-free 0.232
4ZPK Crystal Structure of the Heterodimeric HIF-2a:ARNT Complex with HRE DNA Deposited 2015-05-08	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 3–361（359 aa） Fragment：UNP residues 3-361	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；289 K；4% Tacsimate, pH 6.0, 10% PEG3350	Resolution 3.60 Å R-free 0.321
4ZQD Crystal Structure of the Heterodimeric HIF-2a:ARNT Complex with the Benzoxadiazole Antagonist 0X3 Deposited 2015-05-09	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 3–361（359 aa） Fragment：UNP residues 3-361	Not recorded	0X3 N-(3-chloro-5-fluorophenyl)-4-nitro-2,1,3-benzoxadiazol-5-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；2% Tacsimate, pH 7.0, 6% PEG3350	Resolution 2.87 Å R-free 0.254
4ZQD Crystal Structure of the Heterodimeric HIF-2a:ARNT Complex with the Benzoxadiazole Antagonist 0X3 Deposited 2015-05-09	Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 3–361（359 aa） Fragment：UNP residues 3-361	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；2% Tacsimate, pH 7.0, 6% PEG3350	Resolution 2.87 Å R-free 0.254
6E3S Crystal Structure of the Heterodimeric HIF-2 Complex with Antagonist PT2385 Deposited 2018-07-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 3–362（360 aa）	Mutation：W318A	79A 3-{[(1S)-2,2-difluoro-1-hydroxy-7-(methylsulfonyl)-2,3-dihydro-1H-inden-4-yl]oxy}-5-fluorobenzonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；2% TACSIMATE, PH 7.0, 6% PEG3350	Resolution 3.00 Å R-free 0.249
6E3T Crystal Structure of the Heterodimeric HIF-2 Complex with Antagonist T1001 Deposited 2018-07-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 3–362（360 aa）	Not recorded	HO7 (6S)-6-(4-bromophenyl)-2,3,5,6-tetrahydroimidazo[2,1-b][1,3]thiazole × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；2% TACSIMATE, PH 7.0, 6% PEG3350	Resolution 3.00 Å R-free 0.306
6E3U Crystal Structure of the Heterodimeric HIF-2 Complex with Agonist M1001 Deposited 2018-07-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 3–362（360 aa）	Mutation：W318A	HNJ 3-{[2-(pyrrolidin-1-yl)phenyl]amino}-1H-1lambda~6~,2-benzothiazole-1,1-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2% TACSIMATE, PH 7.0, 6% PEG3350	Resolution 2.85 Å R-free 0.258
7W80 Crystal Structure of the Heterodimeric HIF-2 in Complex with Antagonist Belzutifan Deposited 2021-12-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 3–361（359 aa）	Not recorded	72Q 3-{[(1S,2S,3R)-2,3-difluoro-1-hydroxy-7-(methylsulfonyl)-2,3-dihydro-1H-inden-4-yl]oxy}-5-fluorobenzonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；Tacsimate, PEG3350	Resolution 2.75 Å R-free 0.274
8VHG Structure of the BMAL1/HIF2A heterodimer in Complex with DNA Deposited 2024-01-01	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 3–361（359 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9LJX Crystal Structure of the Heterodimeric HIF-2 Complex with Agonist SD-26 Deposited 2025-01-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 3–362（360 aa）	Not recorded	A1EKB 4-fluoranyl-~{N}-(3-fluoranyl-2-pyrrolidin-1-yl-phenyl)-1,1-bis(oxidanylidene)-1,2-benzothiazol-3-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；PEG 3350, Succinic Acid pH 7.0	Resolution 2.80 Å R-free 0.268
9LJY Crystal Structure of the Heterodimeric HIF-2 Complex with Agonist SD-14 Deposited 2025-01-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 3–361（359 aa）	Not recorded	A1EJ9 4-chloranyl-1,1-bis(oxidanylidene)-~{N}-(2-pyrrolidin-1-ylphenyl)-1,2-benzothiazol-3-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；PEG 3350, Succinic Acid pH 7.0	Resolution 3.20 Å R-free 0.248
9LOH Crystal Structure of the Heterodimeric HIF-2 Complex with Agonist SD-10 Deposited 2025-01-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 3–362（360 aa）	Not recorded	A1EJ8 4-fluoranyl-1,1-bis(oxidanylidene)-~{N}-(2-pyrrolidin-1-ylphenyl)-1,2-benzothiazol-3-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；PEG 3350, Succinic Acid pH 7.0	Resolution 3.02 Å R-free 0.262
9LOI Crystal Structure of the Heterodimeric HIF-2 Complex with Agonist SD-16 Deposited 2025-01-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 3–362（360 aa）	Not recorded	A1EKA 6-chloranyl-1,1-bis(oxidanylidene)-~{N}-(2-pyrrolidin-1-ylphenyl)-1,2-benzothiazol-3-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；PEG 3350, Succinic Acid pH 7.0	Resolution 2.78 Å R-free 0.275

12 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	EPAS1_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–360； UniProt 3–361 Author chain D； PDBConstruct 2–360； UniProt 3–361

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4zph
Deposition date deposition_date	2015-05-07
Structure title title	Crystal Structure of the Heterodimeric HIF-2a:ARNT Complex with Proflavine
Keywords keywords	HIF-2a, ARNT, bHLH-PAS, Proflavine, PROTEIN TRANSPORT-TRANSCRIPTION complex; PROTEIN TRANSPORT/TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	39.51 Å
Radius of gyration Rg (electron density) rg_electron	39.27 Å
Forward intensity I(0) i0	245726000.00
Molecular weight molecular_weight	126240.0 kDa
Excluded volume excluded_volume	157630 Å³
Envelope volume envelope_volume	217250 Å³
Hydration-shell volume shell_volume	46913 Å³
Envelope diameter envelope_diameter	140.6 Å
Shell Rg shell_rg	44.11 Å
Envelope Rg envelope_rg	38.50 Å
Shape Rg shape_rg	39.28 Å
Total Rg total_rg	39.54 Å
Total atoms total_atoms	8843
Residues n_residues	1092
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	131.7 Å
Rg (real space) rg_real	39.59 Å
Rg uncertainty (real space) rg_real_error	1.18 Å
I(0) (real space) i0_real	2.4570e+08
I(0) uncertainty (real space) i0_real_error	4.9900e+06
Rg (reciprocal space) rg_reciprocal	39.55 Å
I(0) (reciprocal space) i0_reciprocal	245700000.0000
Solution quality estimate total_estimate	0.8859
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	42.8 Å
Skewness Skewness skewness	0.306
Kurtosis Kurtosis kurtosis	-0.490
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	24520000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.914; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.816

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Aryl hydrocarbon receptor nuclear translocator
Molecular weight formula_weight	43437.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	8865

MSSADKERLARENHSEIERRRRNKMTAYITELSDMVPTCSALARKPDKLTILRMAVSHMKSLRGTGNTSTDGSYKPSFLTDQELKHLILEAADGFLFIVSCETGRVVYVSDSVTPVLNQPQSEWFGSTLYDQVHPDDVDKLREQLSTSENALTGRVLDLKTGTVKKEGQQSSMRMCMGSRRSFICRMRCGTSSVDPVSMNRLSFLRNRCRNGLGSVKEGEPHFVVVHCTGYIKAWPPAGVSLPDDDPEAGQGSKFCLVAIGRLQVTSSPNCTDMSNICQPTEFISRHNIEGIFTFVDHRCVATVGYQPQELLGKNIVEFCHPEDQQLLRDSFQQVVKLKGQVLSVMFRFRSKTREWLWMRTSSFTFQNPYSDEIEYIICTNTNV

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	Endothelial PAS domain-containing protein 1
Molecular weight formula_weight	41201.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MADKEKKRSSSELRKEKSRDAARCRRSKETEVFYELAHELPLPHSVSSHLDKASIMRLAISFLRTHKLLSSVCSENESEAEADQQMDNLYLKALEGFIAVVTQDGDMIFLSENISKFMGLTQVELTGHSIFDFTHPCDHEEIRENLTLKNGSGFGKKSKDVSTERDFFMRMKCTVTNRGRTVNLKSATWKVLHCTGQVRVYNNCPPHSSLCGSKEPLLSCLIIMCEPIQHPSHMDIPLDSKTFLSRHSMDMKFTYCDDRILELIGYHPEELLGRSAYEFYHALDSENMTKSHQNLCTKGQVVSGQYRMLAKHGGYVWLETQGTVIYNPRNLQPQCIMCVNYVLSEIEKNDVVFSMDQTES

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli BL21

Entity 3 Entity 3 non-polymer

Description description	PROFLAVIN
Molecular weight formula_weight	209.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	22

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8. Citations (1)

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Unit-cell length a length_a	48.896 Å
Unit-cell length b length_b	76.418 Å
Unit-cell length c length_c	98.345 Å
Unit-cell angle α angle_alpha	89.83 °
Unit-cell angle β angle_beta	89.64 °
Unit-cell angle γ angle_gamma	73.21 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	49.172 Å
R factor r_factor	0.1890
R_work r_work	0.1847
R_free r_free	0.2206

fit	/app/data/saxs_computation/zp/4zph/4zph.fit
pddf	/app/data/pr_computation/zp/4zph/4zph.pr.out
profile	/app/data/saxs_computation/zp/4zph/4zph.dat

Crystal Structure of the Heterodimeric HIF-2a:ARNT Complex with Proflavine

1. Protein Identity and Related Structures Protein Identity & Related Structures

Aryl hydrocarbon receptor nuclear translocator

State in the Current Structure

Other States of the Same Protein in the Database

Endothelial PAS domain-containing protein 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)