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2hv1

HADDOCK structure of ARNT PAS-B Homodimer

Method: SOLUTION NMR Dmax: 53.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 356–470 Chain B； UniProt 356–470 Fragment：C-terminal PAS domain (PAS-B), residues 356-470 No other associated polymer 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

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 2HV1 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 experimental conditions 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 oligomeric state Different experimental conditions 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 experimental method 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
2K7S Human ARNT C-Terminal PAS Domain, 3 Residue IB slip Deposited 2008-08-20 Different construct Different mutation/modification Different oligomeric state Different experimental conditions 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 oligomeric state 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 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 oligomeric state 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 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 oligomeric state Different experimental method 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 oligomeric state 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 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 oligomeric state 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 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 ligand/ion Different experimental method 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 oligomeric state 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 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 oligomeric state 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 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 method 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 experimental method 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 oligomeric state 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 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state 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 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state 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 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 method 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 construct Different mutation/modification Different oligomeric state 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 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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
6D09 Crystal structure of PT2440 bound to HIF2a-B*:ARNT-B* complex Deposited 2018-04-10 Different construct Different mutation/modification Different oligomeric state 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 356–470（115 aa） Fragment：residues 356-470
Mutation：E13R 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
6D09 Crystal structure of PT2440 bound to HIF2a-B*:ARNT-B* complex Deposited 2018-04-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 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
6D0B Crystal structure of PT1614 bound to HIF2a-B*:ARNT-B* complex Deposited 2018-04-10 Different construct Different mutation/modification Different oligomeric state 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 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different experimental method 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 oligomeric state 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 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 oligomeric state 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 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 oligomeric state 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 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 oligomeric state 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 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 oligomeric state 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 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 oligomeric state 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 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 oligomeric state 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 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 oligomeric state 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 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 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）
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 method 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 method 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 method 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 method 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 method 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 method 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 oligomeric state 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 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 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 oligomeric state 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 oligomeric state 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 48 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ARNT_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–119； UniProt 356–470 Author chain B； PDBConstruct 5–119； 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

SAXS profile for 2hv1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2hv1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2hv1
Deposition date deposition_date2006-07-27
Structure title titleHADDOCK structure of ARNT PAS-B Homodimer
Keywords keywordsARNT transcription PAS HADDOCK, TRANSCRIPTION, PROTEIN BINDING; TRANSCRIPTION, PROTEIN BINDING
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier17.60 Å
Radius of gyration Rg (electron density) rg_electron17.36 Å
Forward intensity I(0) i0587888000.00
Molecular weight molecular_weight204670.0 kDa
Excluded volume excluded_volume255730 ų
Envelope volume envelope_volume41214 ų
Hydration-shell volume shell_volume18996 ų
Envelope diameter envelope_diameter58.7 Å
Shell Rg shell_rg24.31 Å
Envelope Rg envelope_rg18.22 Å
Shape Rg shape_rg17.36 Å
Total Rg total_rg17.53 Å
Total atoms total_atoms28448
Residues n_residues1728
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax53.7 Å
Rg (real space) rg_real17.53 Å
Rg uncertainty (real space) rg_real_error0.37 Å
I(0) (real space) i0_real5.8790e+08
I(0) uncertainty (real space) i0_real_error7.5680e+06
Rg (reciprocal space) rg_reciprocal17.54 Å
I(0) (reciprocal space) i0_reciprocal587900000.0000
Solution quality estimate total_estimate0.8275
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.4 Å
Skewness Skewness skewness0.204
Kurtosis Kurtosis kurtosis-0.480
Angular range angular_range— – 0.4500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1601000.0000
Real-space data points n_real_points76
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.923; Stabil: 0.995; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2hv1a_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.110 — Profilin-like
Superfamily Superfamily superfamilyd.110.3 — PYP-like sensor domain (PAS domain)
Family Family familyd.110.3.0 — automated matches
Domain ID domain_idd2hv1b_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.110 — Profilin-like
Superfamily Superfamily superfamilyd.110.3 — PYP-like sensor domain (PAS domain)
Family Family familyd.110.3.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id2hv1A01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology450 — Beta-Lactamase
Homologous superfamily homologous superfamily20 — PAS domain
Domain ID domain_id2hv1B01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology450 — Beta-Lactamase
Homologous superfamily homologous superfamily20 — PAS domain
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8. Citations (1)

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9. Files and Curves (10)