6d09

Crystal structure of PT2440 bound to HIF2a-B:ARNT-B complex

Method: X-RAY DIFFRACTION D_max: 70.5 Å Quality: GOOD

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

Endothelial PAS domain-containing protein 1

Homo sapiens

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 239–350	Fragment：residues 239-350 Mutation：R14E	Aryl hydrocarbon receptor nuclear translocator × 1 （P27540） FOJ 3-{[(3R)-4-(difluoromethyl)-2,2-difluoro-3-hydroxy-1,1-dioxo-2,3-dihydro-1H-1-benzothiophen-5-yl]oxy}-5-fluorobenzonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；50 mM Bis-Tris pH5.4 and 16% PEG3350. Seeding with crushed crystals right after setup	Resolution 1.85 Å R-free 0.282
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 239–350	Fragment：residues 239-350 Mutation：R14E	Aryl hydrocarbon receptor nuclear translocator × 1 （P27540） FOJ 3-{[(3R)-4-(difluoromethyl)-2,2-difluoro-3-hydroxy-1,1-dioxo-2,3-dihydro-1H-1-benzothiophen-5-yl]oxy}-5-fluorobenzonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；50 mM Bis-Tris pH5.4 and 16% PEG3350. Seeding with crushed crystals right after setup	Resolution 1.85 Å R-free 0.282

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 6D09	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1P97 NMR structure of the C-terminal PAS domain of HIF2a Deposited 2003-05-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 240–350（111 aa） Fragment：C-terminal PAS domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.3；303 K；Ionic strength (raw mmCIF value) 15 mM - 75 mM；Pressure ambient NMR sample composition 0.9mM HIF2a (240-350) U-15N,13C; 50 mM Tris buffer, 15 mM NaCl, 5 mM DTT (pH 7.3); 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2A24 HADDOCK Structure of HIF-2a/ARNT PAS-B Heterodimer Deposited 2005-06-21	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 242–348（107 aa） Fragment：C-terminal PAS domain (PAS-B)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；Ionic strength (raw mmCIF value) 50mM Tris, 17mM NaCl, 5mM DTT NMR sample composition 250 micro M (15N)HIF-2alpha PAS-B (240-350) + 1mM ARNT PAS-B (356-470), 50mM Tris (pH=7.5), 17mM NaCl, 5mM DTT NMR sample composition 250 micro M (15N)ARNT PAS-B (356-470) + 1mM HIF-2alpha PAS-B (240-350), 50mM Tris (pH=7.5), 17mM NaCl, 5mM DTT	Resolution not provided
3F1N Crystal structure of a high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains, with internally bound ethylene glycol. Deposited 2008-10-28	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 A 239–350（112 aa） Fragment：HIF2 alpha C-terminal PAS domain	Mutation：R247E	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions vapor diffusion combined with microseeding；pH 6.5；293 K；30% PEG 3350, 0.1M BisTris, 0.05M Tris, 0.017M NaCl, 0.005M DTT, pH 6.5, vapor diffusion combined with microseeding, temperature 293K	Resolution 1.48 Å R-free 0.199
3F1O Crystal structure of the high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains, with an internally-bound artificial ligand Deposited 2008-10-28	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 A 239–350（112 aa） Fragment：HIF2 alpha C-terminal PAS domain	Mutation：R247E	2XY N-[2-nitro-4-(trifluoromethyl)phenyl]morpholin-4-amine × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions vapor diffusion combined with microseeding；pH 6.5；293 K；30% PEG 3350, 0.1M BisTris, 0.05M Tris, 0.017M NaCl, 0.005M DTT , pH 6.5, vapor diffusion combined with microseeding, temperature 293K	Resolution 1.60 Å R-free 0.203
3F1P Crystal structure of a high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains Deposited 2008-10-28	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 A 239–350（112 aa） Fragment：HIF2 alpha C-terminal PAS domain	Mutation：R247E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions vapor diffusion combined with microseeding；pH 6.5；293 K；30% PEG3350, 0.1M BisTris, 0.05M Tris, 0.017M NaCl, 0.005M DTT, pH 6.5, vapor diffusion combined with microseeding, temperature 293K	Resolution 1.17 Å R-free 0.167
3H7W Crystal structure of the high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains with the artificial ligand THS017 Deposited 2009-04-28	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 A 239–350（112 aa） Fragment：HIF2alpha C-terminal PAS domain (UNP residues 239 to 350)	Mutation：R247E	018 2-nitro-N-(thiophen-3-ylmethyl)-4-(trifluoromethyl)aniline × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1M BisTris, 17% PEG3350, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.65 Å R-free 0.236
3H82 Crystal structure of the high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains with the artificial ligand THS020 Deposited 2009-04-28	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 A 239–350（112 aa） Fragment：HIF2alpha C-terminal PAS domain (UNP residues 239 to 350)	Mutation：R247E	020 N-(furan-2-ylmethyl)-2-nitro-4-(trifluoromethyl)aniline × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1M BisTris, 25% PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.50 Å R-free 0.234
4GHI Crystal structure of the high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains in complex with a benzoxadiazole antagonist Deposited 2012-08-07	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 A 239–350（112 aa） Fragment：C-terminal PAS domain, UNP residues 239-350	Mutation：R247E	0X3 N-(3-chloro-5-fluorophenyl)-4-nitro-2,1,3-benzoxadiazol-5-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；293 K；20% PEG400 50 mM BisTris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.50 Å R-free 0.196
4GS9 Crystal structure of the high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains in complex with an inactive benzoxadiazole antagonist Deposited 2012-08-27	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 A 239–350（112 aa） Fragment：HIF2 PAS-B domain, UNP residues 239-350	Mutation：R247E	0XB N-(3-fluorophenyl)-4-nitro-2,1,3-benzoxadiazol-5-amine × 1 PE8 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；293 K；20% PEG 3350 50 mM BISTRIS, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.72 Å R-free 0.202
4PKY ARNT/HIF transcription factor/coactivator complex Deposited 2014-05-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 239–350（112 aa） Fragment：C-terminal PAS 2 and PAC domain residues 239-350	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；1.6 M magnesium sulfate, 0.1 M MES pH 6.5, 20% (w/v) ethylene glycol	Resolution 3.20 Å R-free 0.270
4XT2 Crystal structure of the high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains in complex with a tetrazole-containing antagonist Deposited 2015-01-22	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 A 239–350（112 aa） Fragment：C-terminal PAS domain (UNP residues 239-350)	Mutation：R247E	43L (5S,7R)-5,7-bis(3-bromophenyl)-4,5,6,7-tetrahydrotetrazolo[1,5-a]pyrimidine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；2 uL 500 uM protein against 100 mM Bis-Tris, 25% PEG3350	Resolution 1.70 Å R-free 0.192
4XT2 Crystal structure of the high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains in complex with a tetrazole-containing antagonist Deposited 2015-01-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 239–350（112 aa） Fragment：C-terminal PAS domain (UNP residues 239-350)	Mutation：R247E	43L (5S,7R)-5,7-bis(3-bromophenyl)-4,5,6,7-tetrahydrotetrazolo[1,5-a]pyrimidine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；2 uL 500 uM protein against 100 mM Bis-Tris, 25% PEG3350	Resolution 1.70 Å R-free 0.192
5KIZ Solution Structure of a repacked version of HIF-2 alpha PAS-B Deposited 2016-06-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 239–349（111 aa） Fragment：residues 239-349	Mutation：H248F, Y278S, Y281W, G323M, C339A	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 20；Pressure 1 NMR sample composition 0.5 mM [U-99% 13C; U-99% 15N] HIF-2 alpha D1, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
5TBM Crystal structure of PT2385 bound to HIF2a-B:ARNT-B complex Deposited 2016-09-12	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 A 237–348（112 aa） Fragment：UNP residues 237-248	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；pH 5.4；293 K；50 mM Bis-Tris pH5.4, 16% PEG 3350. use freshly crushed crystal as seed.	Resolution 1.85 Å R-free 0.300
5TBM Crystal structure of PT2385 bound to HIF2a-B:ARNT-B complex Deposited 2016-09-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 237–348（112 aa） Fragment：UNP residues 237-248	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；pH 5.4；293 K；50 mM Bis-Tris pH5.4, 16% PEG 3350. use freshly crushed crystal as seed.	Resolution 1.85 Å R-free 0.300
5UFP Crystal structure of PT2399 bound to HIF2a-B:ARNT-B complex Deposited 2017-01-05	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 A 239–348（110 aa） Fragment：UNP residues 239-348	Not recorded	86D 3-({(1S)-7-[(difluoromethyl)sulfonyl]-2,2-difluoro-1-hydroxy-2,3-dihydro-1H-inden-4-yl}oxy)-5-fluorobenzonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；complex of HIF2-B:ARNT-B 10-12 mg/mL in 10 mM Tris-HCl, pH8.0 and 50 mM KCl; Crystallization buffer of 50 mM Bis-Tris, pH5.4 and 16% PEG3350.	Resolution 1.90 Å R-free 0.271
6CZW Crystal structure of PT1940 bound to HIF2a-B:ARNT-B complex Deposited 2018-04-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 239–350（112 aa） Fragment：residues 239-348	Mutation：R14E	FO7 {2-bromo-3-(3-chloro-5-fluorophenoxy)-6-[(difluoromethyl)sulfonyl]phenyl}methanol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；50 mM Bis-Tris pH5.4, 16% PEG 3350. Seed with crushed crystal right after drops are set up	Resolution 1.60 Å R-free 0.251
6CZW Crystal structure of PT1940 bound to HIF2a-B:ARNT-B complex Deposited 2018-04-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 239–350（112 aa） Fragment：residues 239-348	Mutation：R14E	FO7 {2-bromo-3-(3-chloro-5-fluorophenoxy)-6-[(difluoromethyl)sulfonyl]phenyl}methanol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；50 mM Bis-Tris pH5.4, 16% PEG 3350. Seed with crushed crystal right after drops are set up	Resolution 1.60 Å R-free 0.251
6D0B Crystal structure of PT1614 bound to HIF2a-B:ARNT-B complex Deposited 2018-04-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 239–350（112 aa） Fragment：residues 239-350	Mutation：R14E	FOV N-(3-chloro-5-fluorophenyl)-2-nitro-4-(trifluoromethanesulfonyl)aniline × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；Bis-Tris pH5.4, 16% PEG3350. Seeding right after setup using crushed crystals	Resolution 1.60 Å R-free 0.235
6D0B Crystal structure of PT1614 bound to HIF2a-B:ARNT-B complex Deposited 2018-04-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 239–350（112 aa） Fragment：residues 239-350	Mutation：R14E	FOV N-(3-chloro-5-fluorophenyl)-2-nitro-4-(trifluoromethanesulfonyl)aniline × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；Bis-Tris pH5.4, 16% PEG3350. Seeding right after setup using crushed crystals	Resolution 1.60 Å R-free 0.235
6D0C Crystal structure of HIF2a-B:ARNT-B complex Deposited 2018-04-10	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 239–350（112 aa） Fragment：residues 239-350	Mutation：R247E, E362R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；Bis-Tris, pH5.4 and 16% PEG3350, Seeding with crushed crystals right after setup	Resolution 1.50 Å R-free 0.240
6I7Q Structure of pVHL-elongin B-elongin C (VCB) in complex with hydroxylated-HIF-2alpha (523-542) in the C2221 form Deposited 2018-11-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 523–542（20 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；293 K；0.1M Cacodyl-Na pH 5.8, 0.1M Mg formate, 50 mM Cystamine, 22 % PEG3350	Resolution 1.80 Å R-free 0.237
6I7R Structure of pVHL-elongin B-elongin C (VCB) in complex with hydroxylated-HIF-2alpha (523-542) in the P43212 form Deposited 2018-11-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 523–542（20 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.8；293 K；0.1M Cacodyl-Na pH 5.8, 0.1M Mg Formate, 50mM Cystamine, 22% PEG3350	Resolution 1.95 Å R-free 0.203
6X21 Crystal structure of PT1673 bound to HIF2a-B:ARNT-B complex Deposited 2020-05-19	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 A 239–348（110 aa）	Mutation：R247E	UKJ 1-(3-bromo-5-fluorophenoxy)-4-[(difluoromethyl)sulfonyl]-2-nitrobenzene × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；Bis-Tris, pH5.4, 16% PEG3350	Resolution 1.54 Å R-free 0.233
6X28 Crystal structure of PT2243 bound to HIF2a-B:ARNT-B complex Deposited 2020-05-20	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 A 239–348（110 aa）	Mutation：R247E	ULG (1R)-4-(3,5-difluorophenoxy)-7-(trifluoromethyl)-2,3-dihydro-1H-inden-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；Bis-Tris, pH5.4, 16% PEG3350	Resolution 1.92 Å R-free 0.287
6X2H Crystal structure of PT2863 bound to HIF2a-B:ARNT-B complex Deposited 2020-05-20	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 A 239–348（110 aa）	Not recorded	ULD cis-3-({(1S)-7-[dihydroxy(trifluoromethyl)-lambda~4~-sulfanyl]-2,2-difluoro-1-hydroxy-2,3-dihydro-1H-inden-4-yl}oxy)cyclobutane-1-carbonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；Bis-Tris pH5.4, 16% 3350	Resolution 2.00 Å R-free 0.258
6X37 Crystal structure of PT3245 bound to HIF2a-B:ARNT-B complex Deposited 2020-05-21	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 A 239–348（110 aa）	Mutation：R247E	ULS 3-fluoro-5-{[(7R)-7-hydroxy-1-(trifluoromethyl)-6,7-dihydro-5H-cyclopenta[c]pyridin-4-yl]oxy}benzonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；Bis-Tris, pH5.4, 16% PEG 3350	Resolution 1.94 Å R-free 0.282
6X3D Crystal structure of PT3388 bound to HIF2a-B:ARNT-B complex Deposited 2020-05-21	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 A 239–348（110 aa）	Mutation：R247E	ULM (6R,7S)-4-[(3,3-difluorocyclobutyl)oxy]-6-fluoro-1-(trifluoromethyl)-6,7-dihydro-5H-cyclopenta[c]pyridin-7-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；Bis-Tris, pH5.4 and 16% PEG 3350	Resolution 2.00 Å R-free 0.277
7Q5V HIF PROLYL HYDROXYLASE 2 (PHD2/EGLN1) IN COMPLEX WITH N-OXALYLGLYCINE (NOG) AND HIF-2 ALPHA CODD (523-542) Deposited 2021-11-04	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 523–542（20 aa）	Not recorded	MN MANGANESE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 PEG DI(HYDROXYETHYL)ETHER × 3 GOL GLYCEROL × 1 FMT FORMIC ACID × 3 CL CHLORIDE ION × 1 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；Sample: 1.0 mM PHD2, 1.2 mM MnCl2, 2.0 mM NOG, 2 mM 3C, 2-4 mM HIF-2alpha-CODD; Reservoir: 0.31 M Magnesium formate (range: 0.25-0.39 M), 16.6% w/v polyethylene glycol 3350 (range: 18-22%); Sitting drop (200 nl): protein-to-well ratio, 1:1; Cryo-protectant: 15% v/v dilution of reservoir with glycerol	Resolution 1.17 Å R-free 0.179
7Q5X HIF PROLYL HYDROXYLASE 2 (PHD2/EGLN1) IN COMPLEX WITH 2-OXOGLUTARATE (2OG) AND HIF-2 ALPHA CODD (523-542) Deposited 2021-11-04	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 523–542（20 aa）	Not recorded	MN MANGANESE (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 PEG DI(HYDROXYETHYL)ETHER × 1 FMT FORMIC ACID × 11 GOL GLYCEROL × 1 MG MAGNESIUM ION × 3 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；Sample: 1.0 mM PHD2, 1.2 mM MnCl2, 2.0 mM 2OG, 2 mM 3C, 2-4 mM HIF-2alpha-CODD; Reservoir: 0.33 M Magnesium formate (range: 0.25-0.39 M), 17.5% w/v polyethylene glycol 3350 (range: 18-22%); Sitting drop (200 nl): protein-to-well ratio, 1:1; Cryo-protectant: 15% v/v dilution of reservior solution with glycerol	Resolution 1.21 Å R-free 0.176
7UJV Structure of PHD2 in complex with HIF2a-CODD Deposited 2022-03-31	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 A 523–542（20 aa） Fragment：CODD Peptide	Non-standard monomer：Yes (specific site not provided by mmCIF)	OGA N-OXALYLGLYCINE × 1 GOL GLYCEROL × 1 FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；32.5% (w/v) PEG 2000 MME	Resolution 1.80 Å R-free 0.213
8CK3 STRUCTURE OF HIF2A-ARNT HETERODIMER IN COMPLEX WITH (S)-1-(3,5-Difluoro-phenyl)-5,5-difluoro-3-methanesulfonyl-5,6-dihydro-4H-cyclopenta[c]thiophen-4-ol Deposited 2023-02-14	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 A 239–350（112 aa）	Not recorded	UXU (4~{S})-1-[3,5-bis(fluoranyl)phenyl]-5,5-bis(fluoranyl)-3-methylsulfonyl-4,6-dihydrocyclopenta[c]thiophen-4-ol × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22% PEG 3350, 0.1 M BIS TRIS pH 6.0	Resolution 1.71 Å R-free 0.227
8CK4 STRUCTURE OF HIF2A-ARNT HETERODIMER IN COMPLEX WITH (4S)-1-(3,5-difluorophenyl)-5,5-difluoro-3-methanesulfonyl-4,5,6,7-tetrahydro-2-benzothiophen-4-ol Deposited 2023-02-14	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 A 239–350（112 aa）	Not recorded	UY3 (4~{S})-1-[3,5-bis(fluoranyl)phenyl]-5,5-bis(fluoranyl)-3-methylsulfonyl-6,7-dihydro-4~{H}-2-benzothiophen-4-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；17% (w/v) PEG3350 ; 0.1 M BisTris pH 6.25	Resolution 2.29 Å R-free 0.251
8CK8 STRUCTURE OF HIF2A-ARNT HETERODIMER IN COMPLEX WITH (S)-1-Cyclohexyloxy-5,5-difluoro-3-methanesulfonyl-5,6-dihydro-4H-cyclopenta[c]thiophen-4-ol Deposited 2023-02-14	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 A 239–350（112 aa）	Not recorded	UYF (4~{S})-1-cyclohexyloxy-5,5-bis(fluoranyl)-3-methylsulfonyl-4,6-dihydrocyclopenta[c]thiophen-4-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；17% (w/v) PEG3350 ; 0.1 M BisTris pH 6.25	Resolution 2.30 Å R-free 0.276
8Q5S Anaerobic crystal structure of apo-HIF prolyl hydroxylase 2 (PHD2 181-407)in complex with acetate (ACT) and HIF2alpha-CODD peptide Deposited 2023-08-09	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 523–542（20 aa）	Not recorded	ACT ACETATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；(10-35%) PEG 4K, 0.2 M ammonium acetate, 0.1 M sodium ammonium acetate trihydrate pH (4.1-5.6)	Resolution 1.49 Å R-free 0.213
8Q64 Crystal structure of hydroxylated HIF2alpha-CODD peptide (523-542) bound to apo-HIF prolyl hydroxylase 2 (PHD2 181-407) Deposited 2023-08-10	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 523–542（20 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ACT ACETATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；10-35% PEG 4K, 0.2 M ammonium acetate and 0.1 M sodium ammonium acetate trihydrate pH (4.1-5.6)	Resolution 1.36 Å R-free 0.212
8Q6D Anaerobic crystal structure of HIF prolyl hydroxylase 2 (PHD2 181-407) in complex with HIF2alpha-CODD peptide (523-542), Fe(II) and 2-oxoglutarate (2OG) Deposited 2023-08-11	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 523–542（20 aa）	Not recorded	FE FE (III) ION × 1 AKG 2-OXOGLUTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；10-35% PEG 4K, 0.2 ammonium acetate, sodium ammonium acetate trihydrate pH (4.1-5.6)	Resolution 1.40 Å R-free 0.190
8Q6E Aerobic crystal structure of HIF prolyl hydroxylase 2 (PHD2 181-407) in complex with Fe(III), 2-oxoglutarate (2OG) and HIF2alpha-CODD peptide Deposited 2023-08-11	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 523–542（20 aa）	Not recorded	MG MAGNESIUM ION × 3 CL CHLORIDE ION × 2 FE FE (III) ION × 1 AKG 2-OXOGLUTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；(10-35%) PEG 4K, 0.2 M ammonium acetate , 0.1 M sodium ammonium acetate trihydrate pH (4.1-5.6)	Resolution 1.37 Å R-free 0.205
8RUT HIF prolyl-hydroxylase-2 (PHD2) T387V variant bound to Fe(III), 2-oxoglutarate (2OG) and Hypoxia-inducible Factor-2alpha (HIF-2alpha) Deposited 2024-01-31	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 523–542（20 aa）	Not recorded	ACT ACETATE ION × 1 AKG 2-OXOGLUTARIC ACID × 1 FE FE (III) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；296 K；(10-35%) PEG 4K, 0.2 M ammonium acetate and 0.1 M sodium ammonium acetate trihydrate pH (4.1-5.6).	Resolution 1.62 Å R-free 0.219
8RUV HIF prolyl hydroxylase 2 (PHD2) T387I variant bound to Fe(III), 2-oxoglutarate (2OG) and Hypoxia-inducible Factor 2alpha (HIF2alpha) Deposited 2024-01-31	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 524–542（19 aa）	Not recorded	FE FE (III) ION × 1 AKG 2-OXOGLUTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；297 K；(10-35%) PEG 4K, 0.2 M ammonium acetate and 0.1 M sodium ammonium acetate trihydrate pH (4.1-5.6).	Resolution 1.66 Å R-free 0.257
8RUZ Anaerobic HIF prolyl-hydroxylase-2 (PHD2) T387S variant bound to acetate (ACT) and Hypoxia-inducible Factor-2alpha (HIF-2alpha) Deposited 2024-01-31	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 524–542（19 aa）	Not recorded	ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；297 K；(10-35%) PEG 4K, 0.2 M ammonium acetate and 0.1 M sodium ammonium acetate trihydrate pH (4.1-5.6).	Resolution 1.82 Å R-free 0.314
8RV1 HIF prolyl hydroxylase 2 (PHD2) T387S variant bound to acetate (ACT) and hydroxylated Hypoxia-inducible Factor 2alpha (HIF2alpha) Deposited 2024-01-31	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 523–542（20 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；297 K；(10-35%) PEG 4K, 0.2 M ammonium acetate and 0.1 M sodium ammonium acetate trihydrate pH (4.1-5.6).	Resolution 1.39 Å R-free 0.191
9I64 Crystal structure of Casdatifan bound to HIF2a-B:ARNT-B complex Deposited 2025-01-29	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 A 240–350（111 aa）	Not recorded	A1I0H (5~{R},6~{S},8~{R})-3,5,6-tris(fluoranyl)-8-[(1~{S},2~{R})-2-fluoranyl-7-methylsulfonyl-1-oxidanyl-2,3-dihydro-1~{H}-inden-4-yl]-5,6,7,8-tetrahydronaphthalene-1-carbonitrile × 1 FMT FORMIC ACID × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.10 M Sodium Acetate, 1.25 M Sodium Fluoride	Resolution 1.56 Å R-free 0.214
9OF0 Cryo-EM Structure of Human HIF-2a-ARNT Complexed on 20-bp HRE Deposited 2025-04-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 5–361（357 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；50mM HEPES, 150mM NaCl, 5mM MgCl2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9OF2 Dimer of HIF-2a-ARNT Heterodimers Complexed on 51-bp HRE/HAS Deposited 2025-04-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain C 5–361（357 aa） Chain E 5–361（357 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；50mM HEPES, 150mM NaCl, 5mM MgCl2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

41 other PDB entries and 45 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	EPAS1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–117； UniProt 239–350

Aryl hydrocarbon receptor nuclear translocator

Homo sapiens

UniProt P27540

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 356–470	Fragment：residues 356-470 Mutation：E13R	Endothelial PAS domain-containing protein 1 × 1 （Q99814） FOJ 3-{[(3R)-4-(difluoromethyl)-2,2-difluoro-3-hydroxy-1,1-dioxo-2,3-dihydro-1H-1-benzothiophen-5-yl]oxy}-5-fluorobenzonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；50 mM Bis-Tris pH5.4 and 16% PEG3350. Seeding with crushed crystals right after setup	Resolution 1.85 Å R-free 0.282
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 356–470	Fragment：residues 356-470 Mutation：E13R	Endothelial PAS domain-containing protein 1 × 1 （Q99814） FOJ 3-{[(3R)-4-(difluoromethyl)-2,2-difluoro-3-hydroxy-1,1-dioxo-2,3-dihydro-1H-1-benzothiophen-5-yl]oxy}-5-fluorobenzonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；50 mM Bis-Tris pH5.4 and 16% PEG3350. Seeding with crushed crystals right after setup	Resolution 1.85 Å R-free 0.282

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6D09	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1X0O human ARNT C-terminal PAS domain Deposited 2005-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 356–470（115 aa） Fragment：C-TERMINAL PAS DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 17mM NaCl；Pressure ambient NMR measurement conditions pH 6.6；310 K；Ionic strength (raw mmCIF value) 17mM NaCl；Pressure ambient NMR sample composition 1mM hARNT C-term PAS Domain U-15N,13C; 50mM Tris buffer; 17mM NaCl, 5mM DTT \| 90% H2O/10% D2O NMR sample composition 0.478mM hARNT C-term PAS Domain U-15N; 50mM Tris buffer; 17mM NaCl, 5mM DTT \| 93% H2O/7% D2O	Resolution not provided
2A24 HADDOCK Structure of HIF-2a/ARNT PAS-B Heterodimer Deposited 2005-06-21	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 358–465（108 aa） Fragment：C-terminal PAS domain (PAS-B)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；Ionic strength (raw mmCIF value) 50mM Tris, 17mM NaCl, 5mM DTT NMR sample composition 250 micro M (15N)HIF-2alpha PAS-B (240-350) + 1mM ARNT PAS-B (356-470), 50mM Tris (pH=7.5), 17mM NaCl, 5mM DTT NMR sample composition 250 micro M (15N)ARNT PAS-B (356-470) + 1mM HIF-2alpha PAS-B (240-350), 50mM Tris (pH=7.5), 17mM NaCl, 5mM DTT	Resolution not provided
2B02 Crystal Structure of ARNT PAS-B Domain Deposited 2005-09-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 354–470（117 aa） Fragment：PAS-B Domain	Mutation：C358S Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.65；295 K；Ammonium sulfate, PEG 400, HEPES, pH 8.65, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.50 Å R-free 0.208
2HV1 HADDOCK structure of ARNT PAS-B Homodimer Deposited 2006-07-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 356–470（115 aa） Fragment：C-terminal PAS domain (PAS-B), residues 356-470 Chain B 356–470（115 aa） Fragment：C-terminal PAS domain (PAS-B), residues 356-470	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 50mM Tris, 17mM NaCl NMR sample composition 1mM down to 125 micro M (15N) ARNT PAS-B, 50mM Tris, 17mM NaCl, 5mM DTT NMR sample composition 75 micro M (15N) ARNT PAS-B, 400 micro M ARNT PAS-B with CMSTL spin label attached (to C358 or C451), 50mM Tris, 17mM NaCl	Resolution not provided
2K7S Human ARNT C-Terminal PAS Domain, 3 Residue IB slip Deposited 2008-08-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 356–470（115 aa） Fragment：ARNT PAS-B	Mutation：F444Q, F446A, Y456T	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 17；Pressure ambient NMR sample composition 900 uM [U-98% 13C; U-98% 15N] ARNT PAS-B Slipped IB Strand, 50 mM TRIS, 17 mM sodium chloride, 5 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3F1N Crystal structure of a high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains, with internally bound ethylene glycol. Deposited 2008-10-28	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 356–470（115 aa） Fragment：ARNT C-terminal PAS domain	Mutation：E362R	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions vapor diffusion combined with microseeding；pH 6.5；293 K；30% PEG 3350, 0.1M BisTris, 0.05M Tris, 0.017M NaCl, 0.005M DTT, pH 6.5, vapor diffusion combined with microseeding, temperature 293K	Resolution 1.48 Å R-free 0.199
3F1O Crystal structure of the high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains, with an internally-bound artificial ligand Deposited 2008-10-28	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 356–470（115 aa） Fragment：ARNT C-terminal PAS domain	Mutation：E362R	2XY N-[2-nitro-4-(trifluoromethyl)phenyl]morpholin-4-amine × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions vapor diffusion combined with microseeding；pH 6.5；293 K；30% PEG 3350, 0.1M BisTris, 0.05M Tris, 0.017M NaCl, 0.005M DTT , pH 6.5, vapor diffusion combined with microseeding, temperature 293K	Resolution 1.60 Å R-free 0.203
3F1P Crystal structure of a high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains Deposited 2008-10-28	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 356–470（115 aa） Fragment：ARNT C-terminal PAS domain	Mutation：E362R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions vapor diffusion combined with microseeding；pH 6.5；293 K；30% PEG3350, 0.1M BisTris, 0.05M Tris, 0.017M NaCl, 0.005M DTT, pH 6.5, vapor diffusion combined with microseeding, temperature 293K	Resolution 1.17 Å R-free 0.167
3H7W Crystal structure of the high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains with the artificial ligand THS017 Deposited 2009-04-28	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 356–470（115 aa） Fragment：ARNT C-terminal PAS domain (UNP residues 356 to 470)	Mutation：E362R	018 2-nitro-N-(thiophen-3-ylmethyl)-4-(trifluoromethyl)aniline × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1M BisTris, 17% PEG3350, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.65 Å R-free 0.236
3H82 Crystal structure of the high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains with the artificial ligand THS020 Deposited 2009-04-28	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 356–470（115 aa） Fragment：ARNT C-terminal PAS domain (UNP residues 356 to 470)	Mutation：E362R	020 N-(furan-2-ylmethyl)-2-nitro-4-(trifluoromethyl)aniline × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1M BisTris, 25% PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.50 Å R-free 0.234
4EQ1 Crystal Structure of the ARNT PAS-B homodimer Deposited 2012-04-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 357–464（108 aa） Fragment：PAS-B domain (UNP residues 357-464) Chain B 357–464（108 aa） Fragment：PAS-B domain (UNP residues 357-464)	Not recorded	PE5 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；2M Ammonium Sulfate, 3% PEG400, 1% PEI, 50mM Tris pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.227
4GHI Crystal structure of the high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains in complex with a benzoxadiazole antagonist Deposited 2012-08-07	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 356–470（115 aa） Fragment：C-terminal PAS domain, UNP residues 356-470	Mutation：E362R	0X3 N-(3-chloro-5-fluorophenyl)-4-nitro-2,1,3-benzoxadiazol-5-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；293 K；20% PEG400 50 mM BisTris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.50 Å R-free 0.196
4GS9 Crystal structure of the high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains in complex with an inactive benzoxadiazole antagonist Deposited 2012-08-27	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 356–470（115 aa） Fragment：ARNT PAS-B domain, UNP residues 356-470	Mutation：E362R	0XB N-(3-fluorophenyl)-4-nitro-2,1,3-benzoxadiazol-5-amine × 1 PE8 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；293 K；20% PEG 3350 50 mM BISTRIS, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.72 Å R-free 0.202
4H6J Identification of Cys 255 in HIF-1 as a novel site for development of covalent inhibitors of HIF-1 /ARNT PasB domain protein-protein interaction. Deposited 2012-09-19	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 357–470（114 aa） Fragment：PAS-B DOMAIN, UNP residues 357-470	Mutation：E362R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；20% PEG 8000, 0.2M MgCl2, 0.1M Tris pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.52 Å R-free 0.248
4LPZ ARNT transcription factor/coactivator complex Deposited 2013-07-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 356–470（115 aa） Fragment：PAS 2 and PAC domain residues 356-470 Chain B 356–470（115 aa） Fragment：PAS 2 and PAC domain residues 356-470	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1M Succinic acid, 30% w/v D-Sorbitol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.15 Å R-free 0.272
4PKY ARNT/HIF transcription factor/coactivator complex Deposited 2014-05-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 342–456（115 aa） Fragment：C-terminal PAS 2 domain residues 342-456	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；1.6 M magnesium sulfate, 0.1 M MES pH 6.5, 20% (w/v) ethylene glycol	Resolution 3.20 Å R-free 0.270
4PKY ARNT/HIF transcription factor/coactivator complex Deposited 2014-05-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 342–456（115 aa） Fragment：C-terminal PAS 2 domain residues 342-456	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；1.6 M magnesium sulfate, 0.1 M MES pH 6.5, 20% (w/v) ethylene glycol	Resolution 3.20 Å R-free 0.270
4XT2 Crystal structure of the high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains in complex with a tetrazole-containing antagonist Deposited 2015-01-22	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 342–456（115 aa） Fragment：C-terminal PAS domain (UNP residues 342-456)	Mutation：E362R	43L (5S,7R)-5,7-bis(3-bromophenyl)-4,5,6,7-tetrahydrotetrazolo[1,5-a]pyrimidine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；2 uL 500 uM protein against 100 mM Bis-Tris, 25% PEG3350	Resolution 1.70 Å R-free 0.192
4XT2 Crystal structure of the high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains in complex with a tetrazole-containing antagonist Deposited 2015-01-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 342–456（115 aa） Fragment：C-terminal PAS domain (UNP residues 342-456)	Mutation：E362R	43L (5S,7R)-5,7-bis(3-bromophenyl)-4,5,6,7-tetrahydrotetrazolo[1,5-a]pyrimidine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；2 uL 500 uM protein against 100 mM Bis-Tris, 25% PEG3350	Resolution 1.70 Å R-free 0.192
5TBM Crystal structure of PT2385 bound to HIF2a-B:ARNT-B complex Deposited 2016-09-12	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 340–453（114 aa） Fragment：UNP residues 340-453	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；pH 5.4；293 K；50 mM Bis-Tris pH5.4, 16% PEG 3350. use freshly crushed crystal as seed.	Resolution 1.85 Å R-free 0.300
5TBM Crystal structure of PT2385 bound to HIF2a-B:ARNT-B complex Deposited 2016-09-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 340–453（114 aa） Fragment：UNP residues 340-453	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；pH 5.4；293 K；50 mM Bis-Tris pH5.4, 16% PEG 3350. use freshly crushed crystal as seed.	Resolution 1.85 Å R-free 0.300
5UFP Crystal structure of PT2399 bound to HIF2a-B:ARNT-B complex Deposited 2017-01-05	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 342–453（112 aa） Fragment：UNP residues 342-453	Not recorded	86D 3-({(1S)-7-[(difluoromethyl)sulfonyl]-2,2-difluoro-1-hydroxy-2,3-dihydro-1H-inden-4-yl}oxy)-5-fluorobenzonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；complex of HIF2-B:ARNT-B 10-12 mg/mL in 10 mM Tris-HCl, pH8.0 and 50 mM KCl; Crystallization buffer of 50 mM Bis-Tris, pH5.4 and 16% PEG3350.	Resolution 1.90 Å R-free 0.271
5V0L Crystal structure of the AHR-ARNT heterodimer in complex with the DRE Deposited 2017-02-28	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 A 70–346（277 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 2 CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；277 K；10%-12% PEG 20000, 4-6% Tacsimate pH 7.0 or 0.1 M Bis-Tris pH 6.5	Resolution 4.00 Å R-free 0.323
6CZW Crystal structure of PT1940 bound to HIF2a-B:ARNT-B complex Deposited 2018-04-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 356–470（115 aa） Fragment：residues 356-470	Mutation：E13R	FO7 {2-bromo-3-(3-chloro-5-fluorophenoxy)-6-[(difluoromethyl)sulfonyl]phenyl}methanol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；50 mM Bis-Tris pH5.4, 16% PEG 3350. Seed with crushed crystal right after drops are set up	Resolution 1.60 Å R-free 0.251
6CZW Crystal structure of PT1940 bound to HIF2a-B:ARNT-B complex Deposited 2018-04-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 356–470（115 aa） Fragment：residues 356-470	Mutation：E13R	FO7 {2-bromo-3-(3-chloro-5-fluorophenoxy)-6-[(difluoromethyl)sulfonyl]phenyl}methanol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；50 mM Bis-Tris pH5.4, 16% PEG 3350. Seed with crushed crystal right after drops are set up	Resolution 1.60 Å R-free 0.251
6D0B Crystal structure of PT1614 bound to HIF2a-B:ARNT-B complex Deposited 2018-04-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 356–470（115 aa） Fragment：residues 356-470	Mutation：E13R	FOV N-(3-chloro-5-fluorophenyl)-2-nitro-4-(trifluoromethanesulfonyl)aniline × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；Bis-Tris pH5.4, 16% PEG3350. Seeding right after setup using crushed crystals	Resolution 1.60 Å R-free 0.235
6D0B Crystal structure of PT1614 bound to HIF2a-B:ARNT-B complex Deposited 2018-04-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 356–470（115 aa） Fragment：residues 356-470	Mutation：E13R	FOV N-(3-chloro-5-fluorophenyl)-2-nitro-4-(trifluoromethanesulfonyl)aniline × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；Bis-Tris pH5.4, 16% PEG3350. Seeding right after setup using crushed crystals	Resolution 1.60 Å R-free 0.235
6D0C Crystal structure of HIF2a-B:ARNT-B complex Deposited 2018-04-10	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 356–470（115 aa） Fragment：residues 356-470	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；Bis-Tris, pH5.4 and 16% PEG3350, Seeding with crushed crystals right after setup	Resolution 1.50 Å R-free 0.240
6X21 Crystal structure of PT1673 bound to HIF2a-B:ARNT-B complex Deposited 2020-05-19	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 356–467（112 aa）	Mutation：E362R	UKJ 1-(3-bromo-5-fluorophenoxy)-4-[(difluoromethyl)sulfonyl]-2-nitrobenzene × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；Bis-Tris, pH5.4, 16% PEG3350	Resolution 1.54 Å R-free 0.233
6X28 Crystal structure of PT2243 bound to HIF2a-B:ARNT-B complex Deposited 2020-05-20	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 356–467（112 aa）	Mutation：E362R	ULG (1R)-4-(3,5-difluorophenoxy)-7-(trifluoromethyl)-2,3-dihydro-1H-inden-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；Bis-Tris, pH5.4, 16% PEG3350	Resolution 1.92 Å R-free 0.287
6X2H Crystal structure of PT2863 bound to HIF2a-B:ARNT-B complex Deposited 2020-05-20	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 356–467（112 aa）	Not recorded	ULD cis-3-({(1S)-7-[dihydroxy(trifluoromethyl)-lambda~4~-sulfanyl]-2,2-difluoro-1-hydroxy-2,3-dihydro-1H-inden-4-yl}oxy)cyclobutane-1-carbonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；Bis-Tris pH5.4, 16% 3350	Resolution 2.00 Å R-free 0.258
6X37 Crystal structure of PT3245 bound to HIF2a-B:ARNT-B complex Deposited 2020-05-21	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 356–467（112 aa）	Mutation：E362R	ULS 3-fluoro-5-{[(7R)-7-hydroxy-1-(trifluoromethyl)-6,7-dihydro-5H-cyclopenta[c]pyridin-4-yl]oxy}benzonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；Bis-Tris, pH5.4, 16% PEG 3350	Resolution 1.94 Å R-free 0.282
6X3D Crystal structure of PT3388 bound to HIF2a-B:ARNT-B complex Deposited 2020-05-21	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 342–453（112 aa）	Mutation：E362R	ULM (6R,7S)-4-[(3,3-difluorocyclobutyl)oxy]-6-fluoro-1-(trifluoromethyl)-6,7-dihydro-5H-cyclopenta[c]pyridin-7-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；Bis-Tris, pH5.4 and 16% PEG 3350	Resolution 2.00 Å R-free 0.277
8CK3 STRUCTURE OF HIF2A-ARNT HETERODIMER IN COMPLEX WITH (S)-1-(3,5-Difluoro-phenyl)-5,5-difluoro-3-methanesulfonyl-5,6-dihydro-4H-cyclopenta[c]thiophen-4-ol Deposited 2023-02-14	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 356–470（115 aa）	Not recorded	UXU (4~{S})-1-[3,5-bis(fluoranyl)phenyl]-5,5-bis(fluoranyl)-3-methylsulfonyl-4,6-dihydrocyclopenta[c]thiophen-4-ol × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22% PEG 3350, 0.1 M BIS TRIS pH 6.0	Resolution 1.71 Å R-free 0.227
8CK4 STRUCTURE OF HIF2A-ARNT HETERODIMER IN COMPLEX WITH (4S)-1-(3,5-difluorophenyl)-5,5-difluoro-3-methanesulfonyl-4,5,6,7-tetrahydro-2-benzothiophen-4-ol Deposited 2023-02-14	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 356–470（115 aa）	Not recorded	UY3 (4~{S})-1-[3,5-bis(fluoranyl)phenyl]-5,5-bis(fluoranyl)-3-methylsulfonyl-6,7-dihydro-4~{H}-2-benzothiophen-4-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；17% (w/v) PEG3350 ; 0.1 M BisTris pH 6.25	Resolution 2.29 Å R-free 0.251
8CK8 STRUCTURE OF HIF2A-ARNT HETERODIMER IN COMPLEX WITH (S)-1-Cyclohexyloxy-5,5-difluoro-3-methanesulfonyl-5,6-dihydro-4H-cyclopenta[c]thiophen-4-ol Deposited 2023-02-14	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 356–470（115 aa）	Not recorded	UYF (4~{S})-1-cyclohexyloxy-5,5-bis(fluoranyl)-3-methylsulfonyl-4,6-dihydrocyclopenta[c]thiophen-4-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；17% (w/v) PEG3350 ; 0.1 M BisTris pH 6.25	Resolution 2.30 Å R-free 0.276
8G4A Human ARNT PAS-B complexed with KG-548 small molecule Deposited 2023-02-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 356–470（115 aa） Chain B 356–470（115 aa）	Not recorded	YL8 5-[3,5-bis(trifluoromethyl)phenyl]-2H-tetrazole × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1 M MES pH 6.5, 1.6 M magnesium sulfate, 2:1 (protein:condition)	Resolution 1.97 Å R-free 0.229
8XS6 Crystal structure of the DNA-bound AHR-ARNT heterodimer in complex with Tapinarof Deposited 2024-01-09	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 A 85–465（381 aa）	Not recorded	A1LWH Tapinarof × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；potassium citrate tribasic monohydrate, PEG3350	Resolution 2.95 Å R-free 0.271
8XS7 Crystal structure of the DNA-bound AHR-ARNT heterodimer in complex with FICZ Deposited 2024-01-09	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 A 85–465（381 aa）	Not recorded	DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 A1LWI 5,11-dihydroindolo[3,2-b]carbazole-12-carbaldehyde × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；potassium citrate tribasic monohydrate, PEG3350	Resolution 2.77 Å R-free 0.267
8XS8 Crystal structure of the DNA-bound AHR-ARNT heterodimer in complex with Benzo[a]pyrene Deposited 2024-01-09	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 A 85–465（381 aa）	Not recorded	W62 benzo[a]pyrene × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；potassium citrate tribasic monohydrate, PEG3350	Resolution 3.11 Å R-free 0.230
8XS9 Crystal structure of the DNA-bound AHR-ARNT heterodimer in complex with beta-Naphthoflavone Deposited 2024-01-09	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 A 85–465（381 aa）	Not recorded	DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 A1LWJ (3R)-3-phenyl-2,3-dihydrobenzo[f]chromen-1-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；potassium citrate tribasic monohydrate, PEG3350	Resolution 2.80 Å R-free 0.264
8XSA Crystal structure of the DNA-bound AHR-ARNT heterodimer in complex with Indigo Deposited 2024-01-09	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 A 85–465（381 aa）	Not recorded	DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 A1LWK 2-(3-oxidanyl-1H-indol-2-yl)indol-3-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；potassium citrate tribasic monohydrate, PEG3350	Resolution 2.60 Å R-free 0.249
8XSB Crystal structure of the DNA-bound AHR-ARNT heterodimer in complex with Indirubin Deposited 2024-01-09	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 A 85–465（381 aa）	Not recorded	JY6 (3~{Z})-3-(3-oxidanylidene-1~{H}-indol-2-ylidene)-1~{H}-indol-2-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；potassium citrate tribasic monohydrate, PEG3350	Resolution 3.06 Å R-free 0.240
9I64 Crystal structure of Casdatifan bound to HIF2a-B:ARNT-B complex Deposited 2025-01-29	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 355–470（116 aa）	Not recorded	A1I0H (5~{R},6~{S},8~{R})-3,5,6-tris(fluoranyl)-8-[(1~{S},2~{R})-2-fluoranyl-7-methylsulfonyl-1-oxidanyl-2,3-dihydro-1~{H}-inden-4-yl]-5,6,7,8-tetrahydronaphthalene-1-carbonitrile × 1 FMT FORMIC ACID × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.10 M Sodium Acetate, 1.25 M Sodium Fluoride	Resolution 1.56 Å R-free 0.214
9OF0 Cryo-EM Structure of Human HIF-2a-ARNT Complexed on 20-bp HRE Deposited 2025-04-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 91–470（380 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；50mM HEPES, 150mM NaCl, 5mM MgCl2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9OF2 Dimer of HIF-2a-ARNT Heterodimers Complexed on 51-bp HRE/HAS Deposited 2025-04-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain D 91–470（380 aa） Chain F 91–470（380 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；50mM HEPES, 150mM NaCl, 5mM MgCl2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9OFU Dimer of HIF-1a-ARNT Heterodimers Complexed on 52-bp HRE/HAS Deposited 2025-04-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain B 91–470（380 aa） Chain D 91–470（380 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；50mM HEPES, 150mM NaCl, 5mM MgCl2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å

42 other PDB entries and 47 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ARNT_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 7–121； UniProt 356–470

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	6d09
Deposition date deposition_date	2018-04-10
Structure title title	Crystal structure of PT2440 bound to HIF2a-B:ARNT-B complex
Keywords keywords	Hif2a, Pas B domain, ARNT, hypoxia inducible factor, EPAS1, TRANSCRIPTION; 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	19.39 Å
Radius of gyration Rg (electron density) rg_electron	18.70 Å
Forward intensity I(0) i0	12265700.00
Molecular weight molecular_weight	25746.0 kDa
Excluded volume excluded_volume	31962 Å³
Envelope volume envelope_volume	37312 Å³
Hydration-shell volume shell_volume	17107 Å³
Envelope diameter envelope_diameter	73.5 Å
Shell Rg shell_rg	24.53 Å
Envelope Rg envelope_rg	19.24 Å
Shape Rg shape_rg	18.68 Å
Total Rg total_rg	19.61 Å
Total atoms total_atoms	1807
Residues n_residues	217
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	70.5 Å
Rg (real space) rg_real	19.38 Å
Rg uncertainty (real space) rg_real_error	0.58 Å
I(0) (real space) i0_real	1.2270e+07
I(0) uncertainty (real space) i0_real_error	1.6450e+05
Rg (reciprocal space) rg_reciprocal	19.38 Å
I(0) (reciprocal space) i0_reciprocal	12270000.0000
Solution quality estimate total_estimate	0.7627
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.9 Å
Skewness Skewness skewness	0.354
Kurtosis Kurtosis kurtosis	-0.268
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2962000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.684; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.859; Smooth: 0.000

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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	Endothelial PAS domain-containing protein 1
Molecular weight formula_weight	13538.3 kDa
Mutation mutation	R14E
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1846

GEFKGLDSKTFLSEHSMDMKFTYCDDRITELIGYHPEELLGRSAYEFYHALDSENMTKSHQNLCTKGQVVSGQYRMLAKHGGYVWLETQGTVIYNPRNLQPQCIMCVNYVLSEIEKN

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Aryl hydrocarbon receptor nuclear translocator
Molecular weight formula_weight	14243.1 kDa
Mutation mutation	E13R
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GEFKGLNVCQPTRFISRHNIEGIFTFVDHRCVATVGYQPQELLGKNIVEFCHPEDQQLLRDSFQQVVKLKGQVLSVMFRFRSKNQEWLWMRTSSFTFQNPYSDEIEYIICTNTNVKNSSQE

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	3-{[(3R)-4-(difluoromethyl)-2,2-difluoro-3-hydroxy-1,1-dioxo-2,3-dihydro-1H-1-benzothiophen-5-yl]oxy}-5-fluorobenzonitrile
Molecular weight formula_weight	405.3 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	21

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d6d09a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.3 — PYP-like sensor domain (PAS domain)
Family Family family	d.110.3.7 — Hypoxia-inducible factor Hif2a, C-terminal domain

Domain ID domain_id	d6d09a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6d09b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.3 — PYP-like sensor domain (PAS domain)
Family Family family	d.110.3.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	6d09A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	20 — PAS domain

Domain ID domain_id	6d09B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	20 — PAS domain

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8. Citations (1)

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Unit-cell length a length_a	73.216 Å
Unit-cell length b length_b	83.832 Å
Unit-cell length c length_c	41.410 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.25 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	28.840 Å
R factor r_factor	0.2293
R_work r_work	0.2265
R_free r_free	0.2816

fit	/app/data/saxs_computation/d0/6d09/6d09.fit
pddf	/app/data/pr_computation/d0/6d09/6d09.pr.out
profile	/app/data/saxs_computation/d0/6d09/6d09.dat

Crystal structure of PT2440 bound to HIF2a-B:ARNT-B complex

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

Endothelial PAS domain-containing protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Aryl hydrocarbon receptor nuclear translocator

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

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Crystal structure of PT2440 bound to HIF2a-B*:ARNT-B* complex

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

Endothelial PAS domain-containing protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Aryl hydrocarbon receptor nuclear translocator

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

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Crystal structure of PT2440 bound to HIF2a-B:ARNT-B complex