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- PDB-9efa: Chemical inhibition of the N-acetyltaurine amidohydrolase PTER re... -

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Basic information

Entry
Database: PDB / ID: 9efa
TitleChemical inhibition of the N-acetyltaurine amidohydrolase PTER reduces food intake and obesity
ComponentsPhosphotriesterase-related protein
KeywordsHYDROLASE / N-acetyltaurine amidohydrolase
Function / homologyPhosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolase / hydrolase activity / zinc ion binding / Uncharacterized protein
Function and homology information
Biological speciesAmphimedon queenslandica (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFu, S. / Hinshaw, S.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Biorxiv / Year: 2026
Title: A small molecule PTER-selective inhibitor reduces food intake and body weight.
Authors: Fu, S. / Wang, L. / Li, V.L. / Lyu, X. / Wei, W. / Shi, X. / Deng, S. / Barber, J.L. / Tahir, U.A. / Adams, C. / Carson, A. / Hidalgo, B. / Raffield, L.M. / Wilson, J.G. / Razumkov, H. / ...Authors: Fu, S. / Wang, L. / Li, V.L. / Lyu, X. / Wei, W. / Shi, X. / Deng, S. / Barber, J.L. / Tahir, U.A. / Adams, C. / Carson, A. / Hidalgo, B. / Raffield, L.M. / Wilson, J.G. / Razumkov, H. / Xiao, S. / Spaas, J. / Fernandez, D. / Zhang, T. / Gerszten, R.E. / Benson, M.D. / Gray, N.S. / Hinshaw, S.M. / Long, J.Z.
History
DepositionNov 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 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: Phosphotriesterase-related protein
B: Phosphotriesterase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5536
Polymers78,2922
Non-polymers2624
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-160 kcal/mol
Surface area23590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.877, 48.403, 83.230
Angle α, β, γ (deg.)90.000, 96.983, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phosphotriesterase-related protein / Parathion hydrolase-related protein


Mass: 39145.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amphimedon queenslandica (invertebrata)
Gene: 100634509 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X7VMK4
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.11 Å3/Da / Density % sol: 41.82 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 200mM MgCl2, 100mM Tris pH 8.5, and 20%PEG-8k

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.44→31.33 Å / Num. obs: 24168 / % possible obs: 97.45 % / Redundancy: 4.5 % / Rpim(I) all: 0.164 / Net I/σ(I): 4.3
Reflection shellResolution: 2.44→6.6 Å / Num. unique obs: 1182 / CC1/2: 0.172 / Rpim(I) all: 0.991

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→31.117 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.827 / WRfactor Rfree: 0.293 / WRfactor Rwork: 0.213 / SU B: 21.014 / SU ML: 0.401 / Average fsc free: 0.9371 / Average fsc work: 0.9664 / Cross valid method: FREE R-VALUE / ESU R Free: 0.483
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2812 777 4.853 %
Rwork0.2073 15235 -
all0.211 --
obs-16012 96.96 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.852 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å2-1.12 Å2
2--1.979 Å2-0 Å2
3----2.481 Å2
Refinement stepCycle: LAST / Resolution: 2.8→31.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5412 0 4 2 5418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125556
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165355
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.8147540
X-RAY DIFFRACTIONr_angle_other_deg0.5331.76112400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0445702
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.566532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.17610970
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.10510228
X-RAY DIFFRACTIONr_chiral_restr0.070.2854
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026425
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021151
X-RAY DIFFRACTIONr_nbd_refined0.2320.21537
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2120.25966
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22759
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.23030
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0510.25
X-RAY DIFFRACTIONr_metal_ion_refined0.120.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1830.210
X-RAY DIFFRACTIONr_nbd_other0.2480.230
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1620.23
X-RAY DIFFRACTIONr_mcbond_it2.3822.7742808
X-RAY DIFFRACTIONr_mcbond_other2.3782.7742808
X-RAY DIFFRACTIONr_mcangle_it4.0384.9793510
X-RAY DIFFRACTIONr_mcangle_other4.0384.9793511
X-RAY DIFFRACTIONr_scbond_it2.3623.0482748
X-RAY DIFFRACTIONr_scbond_other2.3623.0492749
X-RAY DIFFRACTIONr_scangle_it4.0625.5044030
X-RAY DIFFRACTIONr_scangle_other4.0625.5044031
X-RAY DIFFRACTIONr_lrange_it6.99126.1176544
X-RAY DIFFRACTIONr_lrange_other6.99126.1226543
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.8-2.8720.331540.2610950.26312100.9330.9594.95870.242
2.872-2.950.388530.27510300.28111500.8890.94494.17390.259
2.95-3.0350.372620.2810130.28511640.9150.94592.3540.269
3.035-3.1270.3550.2759750.27610700.9250.94296.26170.257
3.127-3.2290.32490.24310300.24710880.9210.95999.17280.235
3.229-3.3410.354560.2269910.23310530.9190.96399.43020.22
3.341-3.4660.322470.2189430.22310010.9150.96698.90110.216
3.466-3.6050.296460.2098890.2139450.9470.97198.94180.211
3.605-3.7630.279430.1968900.1999480.9430.97798.41770.201
3.763-3.9440.247460.28220.2038780.9520.97198.86110.204
3.944-4.1540.258420.188080.1848590.9560.97998.95230.195
4.154-4.4010.197400.1537580.1558110.9720.98598.3970.169
4.401-4.6980.221400.1566820.1597350.9740.98498.23130.174
4.698-5.0650.268330.1786690.1827180.9610.98297.77160.201
5.065-5.5330.248270.2276040.2286590.960.97495.75110.255
5.533-6.1620.302270.2124920.2175890.9360.9888.11540.234
6.162-7.0690.225140.1695220.175390.9630.98499.44340.188
7.069-8.5490.213160.1534400.1554590.9650.98599.34640.181
8.549-11.6580.14120.1373600.1373740.9870.98999.46520.168
11.658-31.1170.283150.2682220.2682430.9310.95797.53090.359

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