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

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Basic information

Entry
Database: PDB / ID: 9efb
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 / ACETATE ION / 2-AMINOETHANESULFONIC ACID / Uncharacterized protein
Function and homology information
Biological speciesAmphimedon queenslandica (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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

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Assembly

Deposited unit
A: Phosphotriesterase-related protein
B: Phosphotriesterase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,92210
Polymers78,2922
Non-polymers6308
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-151 kcal/mol
Surface area24040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.019, 48.962, 85.302
Angle α, β, γ (deg.)90.000, 98.631, 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-TAU / 2-AMINOETHANESULFONIC ACID


Mass: 125.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H7NO3S
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.21 Å3/Da / Density % sol: 44.44 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 300mM 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: Jul 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.08→42.33 Å / Num. obs: 39356 / % possible obs: 94.3 % / Redundancy: 5.5 % / Rpim(I) all: 0.169 / Net I/σ(I): 4.4
Reflection shellResolution: 2.08→5.64 Å / Num. unique obs: 1754 / CC1/2: 0.319

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→42.216 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.895 / SU B: 13.223 / SU ML: 0.287 / Cross valid method: FREE R-VALUE / ESU R: 0.917 / ESU R Free: 0.333
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2759 1367 5.292 %
Rwork0.1822 24465 -
all0.187 --
obs-25832 94.786 %
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: 36.87 Å2
Baniso -1Baniso -2Baniso -3
1--2.252 Å20 Å2-0.945 Å2
2--2.936 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5426 0 26 281 5733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125598
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165394
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.8167595
X-RAY DIFFRACTIONr_angle_other_deg0.521.76212489
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9885706
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.527532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00710976
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.52210229
X-RAY DIFFRACTIONr_chiral_restr0.070.2859
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026462
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021154
X-RAY DIFFRACTIONr_nbd_refined0.2220.21423
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.25678
X-RAY DIFFRACTIONr_nbtor_refined0.180.22760
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.22955
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2281
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0580.23
X-RAY DIFFRACTIONr_metal_ion_refined0.0750.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2110.29
X-RAY DIFFRACTIONr_nbd_other0.1740.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2830.29
X-RAY DIFFRACTIONr_mcbond_it3.0223.6182821
X-RAY DIFFRACTIONr_mcbond_other3.023.6182821
X-RAY DIFFRACTIONr_mcangle_it4.7916.4963528
X-RAY DIFFRACTIONr_mcangle_other4.7926.4973529
X-RAY DIFFRACTIONr_scbond_it3.5974.1252777
X-RAY DIFFRACTIONr_scbond_other3.5974.1242776
X-RAY DIFFRACTIONr_scangle_it5.8137.3874067
X-RAY DIFFRACTIONr_scangle_other5.8127.3874068
X-RAY DIFFRACTIONr_lrange_it8.84435.4516504
X-RAY DIFFRACTIONr_lrange_other8.86135.2546472
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
2.4-2.4620.343770.30818450.30919910.8920.92196.53440.289
2.462-2.5290.372950.27917610.28419190.9130.93896.7170.261
2.529-2.6020.3251100.25217250.25618910.9230.94997.03860.227
2.602-2.6820.404810.25216920.25918420.9050.95396.25410.229
2.682-2.770.3511180.22415820.23317730.9230.96395.88270.201
2.77-2.8670.305940.21615640.22117370.9370.97195.45190.192
2.867-2.9740.354920.20814200.21716410.9210.97292.13890.183
2.974-3.0950.323880.18911750.19816080.9240.97478.54480.165
3.095-3.2320.283990.18313850.18915530.9460.97895.5570.163
3.232-3.3890.25790.17513530.1814580.9550.98198.21670.161
3.389-3.5710.265610.1713170.17514050.960.98398.07830.162
3.571-3.7860.226660.15912590.16313480.9690.98598.29380.154
3.786-4.0450.222450.14611910.14912580.9650.98798.25120.147
4.045-4.3650.24670.13410610.1411570.9680.98997.49350.143
4.365-4.7770.234460.13210080.13710850.9670.98897.14290.144
4.777-5.3320.214480.1548800.1579800.9760.98294.69390.163
5.332-6.1410.246320.1766590.1798930.9590.98377.37960.189
6.141-7.4810.201310.1616900.1637350.9730.98498.09520.179
7.481-10.4180.199270.1245570.1275930.9810.98998.48230.151
10.418-42.2160.456110.2093410.2153710.9080.96894.87870.29

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