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- PDB-44id: Drosophila AHR PAS-B M284C/Y336L mutant in complex with alpha-nap... -

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Basic information

Entry
Database: PDB / ID: 44id
TitleDrosophila AHR PAS-B M284C/Y336L mutant in complex with alpha-naphthoflavone
ComponentsAhr homolog spineless
KeywordsTRANSCRIPTION / Drosophila AHR homolog / Spineless / PAS-B domain / alpha-naphthoflavone / ligand recognition
Function / homology
Function and homology information


regulation of R7 cell differentiation / antennal development / specification of animal organ identity / imaginal disc-derived leg segmentation / antennal morphogenesis / male courtship behavior / regulation of dendrite morphogenesis / intracellular receptor signaling pathway / xenobiotic metabolic process / memory ...regulation of R7 cell differentiation / antennal development / specification of animal organ identity / imaginal disc-derived leg segmentation / antennal morphogenesis / male courtship behavior / regulation of dendrite morphogenesis / intracellular receptor signaling pathway / xenobiotic metabolic process / memory / protein heterodimerization activity / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / DNA-templated transcription / nucleus / cytosol
Similarity search - Function
Aryl hydrocarbon receptor/Aryl hydrocarbon receptor repressor / PAS fold-3 / PAS fold / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold ...Aryl hydrocarbon receptor/Aryl hydrocarbon receptor repressor / PAS fold-3 / PAS fold / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
2-PHENYL-4H-BENZO[H]CHROMEN-4-ONE / Ahr homolog spineless
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsDai, S.Y. / Tang, J.M.
Funding support China, 1items
OrganizationGrant numberCountry
Other government2021RC2034 China
CitationJournal: To Be Published
Title: ARNT association reshapes ligand recognition by AHR PAS-B domain
Authors: Dai, S.Y. / Tang, J.M.
History
DepositionJul 30, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ahr homolog spineless
B: Ahr homolog spineless
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0124
Polymers27,4672
Non-polymers5452
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-14 kcal/mol
Surface area11490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.307, 60.307, 120.023
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Ahr homolog spineless


Mass: 13733.611 Da / Num. of mol.: 2 / Fragment: PAS-B domain / Mutation: M284C/Y336L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: ss, CG6993 / Production host: Escherichia coli (E. coli) / References: UniProt: O61543
#2: Chemical ChemComp-BHF / 2-PHENYL-4H-BENZO[H]CHROMEN-4-ONE / 7,8-BENZOFLAVONE / ALPHA-NAPHTHOFLAVONE


Mass: 272.297 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H12O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl PH7.0, 0.2 M NaCl, and 0.8 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.975 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 23, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.5→34.76 Å / Num. obs: 32818 / % possible obs: 91.8 % / Redundancy: 6.9 % / CC1/2: 0.99 / Net I/σ(I): 15.6
Reflection shellResolution: 1.5→1.55 Å / Num. unique obs: 1653 / CC1/2: 0.71

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Processing

Software
NameVersionClassification
PHENIX("2.1_6048": ???)refinement
PDB_EXTRACTV1.0data extraction
HKL-3000v721data reduction
HKL-3000v721data scaling
PHASERv2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→34.76 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / Phase error: 20.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1922 1656 -
Rwork0.1722 --
obs-32818 91.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.51→34.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1764 0 42 206 2012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111853
X-RAY DIFFRACTIONf_angle_d1.1112499
X-RAY DIFFRACTIONf_dihedral_angle_d18.595651
X-RAY DIFFRACTIONf_chiral_restr0.068260
X-RAY DIFFRACTIONf_plane_restr0.009312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.550.2702790.24191574X-RAY DIFFRACTION56
1.55-1.60.25331170.22422027X-RAY DIFFRACTION73
1.6-1.660.25781460.21662628X-RAY DIFFRACTION94
1.66-1.720.25581580.19942641X-RAY DIFFRACTION95
1.72-1.80.23361550.18662642X-RAY DIFFRACTION96
1.8-1.90.24181460.18212711X-RAY DIFFRACTION96
1.9-2.020.19561320.16942718X-RAY DIFFRACTION96
2.02-2.170.20521410.1642743X-RAY DIFFRACTION97
2.17-2.390.20661430.16672761X-RAY DIFFRACTION97
2.39-2.740.21251400.17592817X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.6118-1.42492.40514.0556-1.41961.9907-0.0359-0.3772-0.19510.33320.0419-0.1071-0.05610.16-0.0280.1153-0.0169-0.00380.1621-0.00690.115-18.249711.781812.9527
22.97440.15370.62085.193-1.72332.208-0.1775-0.5350.09580.4825-0.1346-0.5955-0.20430.40680.20020.1610.0344-0.01960.37150.03010.2301-10.7378.251416.6794
34.7618-1.48963.72380.7584-1.4513.4002-0.35190.43190.58680.0093-0.3073-0.7757-0.25490.89780.59950.19380.03090.00930.36120.11550.3463-11.38336.04985.6585
43.7654-3.0908-0.17752.85740.86532.24730.03740.1621-0.29090.0543-0.04610.33290.3131-0.05970.05550.1438-0.00870.00520.1447-0.00070.0909-28.28525.35025.6692
51.4886-1.10160.25393.2765-0.39991.35130.00530.0011-0.0040.0584-0.0907-0.08750.130.22630.06710.08350.02760.00640.13710.01130.0752-21.43527.95812.9583
68.85891.2883-0.31487.89831.76915.42810.04280.1183-0.84740.0272-0.09-0.05850.2607-0.03520.04590.16060.03210.02060.12770.00590.1649-26.3499-6.2717.1483
74.7215-1.55391.59127.8193-3.20316.31480.11960.4170.257-0.5590.06410.1172-0.2979-0.293-0.15020.12660.02920.01180.13220.03530.1109-20.061412.7233-14.409
82.67930.6195-1.90314.5438-1.48775.18720.14670.06610.2742-0.09160.0290.0701-0.2759-0.0699-0.17220.09350.01650.00390.1298-0.01540.1436-16.972112.4289-8.5007
94.3731-5.9275-4.54319.9556.92815.03260.10990.32540.7707-0.30530.0569-0.72220.06710.2276-0.19490.2811-0.0090.04620.21180.07130.2722-16.830521.4186-18.0395
107.1339-0.4518-0.46545.6582-3.03529.4579-0.21540.04810.0070.1777-0.1607-0.7520.39321.05220.42190.2377-0.04320.09170.3390.00210.3662-11.481522.4949-9.0064
115.3884-5.35321.33726.3505-0.89136.20810.170.0980.9453-0.2486-0.2105-0.4835-0.47890.69140.05420.1639-0.03860.05220.153-0.010.2372-22.042920.0994-2.3846
122.3687-1.7052-0.78235.85520.55783.92340.0467-0.05310.0349-0.25480.00350.0428-0.1108-0.0974-0.08150.0739-0.0071-0.00430.108-0.00870.0767-30.401910.571-3.7489
133.45754.4789-0.13886.86520.06863.96090.07680.08770.3854-0.21080.0421-0.4164-0.23570.2882-0.07320.1267-0.00140.02940.09320.00780.2423-25.701224.3509-9.0058
142.9607-3.47931.12184.4046-0.69511.25950.26740.1728-0.0479-0.4316-0.30030.29350.07510.00910.07830.0734-0.00790.02090.08270.00610.0926-25.958412.459-11.008
153.6485-1.67340.36244.815-1.14243.47840.26850.2612-0.0323-0.2944-0.3726-0.23360.2190.32150.0760.1094-0.00740.01650.1014-0.0280.0825-22.12898.0244-11.6816
167.6510.15241.84729.1004-0.06397.61410.0770.1989-0.0103-0.2929-0.01680.04990.1265-0.0338-0.02130.11440.0181-0.0050.08-0.00510.1167-38.57822.6621-12.0282
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 269 through 280 )
2X-RAY DIFFRACTION2chain 'A' and (resid 281 through 292 )
3X-RAY DIFFRACTION3chain 'A' and (resid 293 through 308 )
4X-RAY DIFFRACTION4chain 'A' and (resid 309 through 326 )
5X-RAY DIFFRACTION5chain 'A' and (resid 327 through 368 )
6X-RAY DIFFRACTION6chain 'A' and (resid 369 through 381 )
7X-RAY DIFFRACTION7chain 'B' and (resid 269 through 276 )
8X-RAY DIFFRACTION8chain 'B' and (resid 277 through 285 )
9X-RAY DIFFRACTION9chain 'B' and (resid 286 through 292 )
10X-RAY DIFFRACTION10chain 'B' and (resid 293 through 301 )
11X-RAY DIFFRACTION11chain 'B' and (resid 302 through 309 )
12X-RAY DIFFRACTION12chain 'B' and (resid 310 through 331 )
13X-RAY DIFFRACTION13chain 'B' and (resid 332 through 342 )
14X-RAY DIFFRACTION14chain 'B' and (resid 343 through 355 )
15X-RAY DIFFRACTION15chain 'B' and (resid 356 through 369 )
16X-RAY DIFFRACTION16chain 'B' and (resid 370 through 381 )

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