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- PDB-10tx: Tissue Non-specific Alkaline Phosphatase -S110A bound to PPi -

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Basic information

Entry
Database: PDB / ID: 10tx
TitleTissue Non-specific Alkaline Phosphatase -S110A bound to PPi
ComponentsAlkaline phosphatase, tissue-nonspecific isozyme
KeywordsHYDROLASE / TNAP
Function / homology
Function and homology information


extracellular membrane-bounded organelle / phosphoamidase / pyridoxal 5'-phosphate metabolic process / phosphoamidase activity / phosphoethanolamine phosphatase activity / response to vitamin B6 / futile creatine cycle / Post-translational modification: synthesis of GPI-anchored proteins / pyridoxal phosphatase activity / developmental process involved in reproduction ...extracellular membrane-bounded organelle / phosphoamidase / pyridoxal 5'-phosphate metabolic process / phosphoamidase activity / phosphoethanolamine phosphatase activity / response to vitamin B6 / futile creatine cycle / Post-translational modification: synthesis of GPI-anchored proteins / pyridoxal phosphatase activity / developmental process involved in reproduction / ADP phosphatase activity / pyrophosphatase activity / inhibition of non-skeletal tissue mineralization / response to macrophage colony-stimulating factor / alkaline phosphatase / cementum mineralization / alkaline phosphatase activity / response to sodium phosphate / inorganic diphosphate phosphatase activity / phosphate ion homeostasis / endochondral ossification / response to vitamin D / bone mineralization / side of membrane / calcium ion homeostasis / response to glucocorticoid / response to insulin / mitochondrial intermembrane space / mitochondrial membrane / positive regulation of cold-induced thermogenesis / extracellular matrix / response to lipopolysaccharide / response to antibiotic / calcium ion binding / ATP hydrolysis activity / : / plasma membrane
Similarity search - Function
Alkaline phosphatase, active site / Alkaline phosphatase active site. / Alkaline phosphatase / Alkaline phosphatase / Alkaline phosphatase homologues / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
CITRATE ANION / PHOSPHATE ION / PYROPHOSPHATE 2- / Alkaline phosphatase, tissue-nonspecific isozyme
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsKrishnan, S.S. / Carroll, B.L. / Guarne, A.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-155941 Canada
CitationJournal: Nature / Year: 2026
Title: Glycerol-driven TNAP activation in thermogenesis and mineralization.
Authors: Hussain, M.F. / Krishnan, S.S. / Carroll, B.L. / Samborska, B. / Mousa, A. / Williamson, A. / Delgado-Martin, M. / Srinivasu, B.Y. / Bunk, J. / Rahbani, J.F. / Oppong, A. / Roesler, A. / ...Authors: Hussain, M.F. / Krishnan, S.S. / Carroll, B.L. / Samborska, B. / Mousa, A. / Williamson, A. / Delgado-Martin, M. / Srinivasu, B.Y. / Bunk, J. / Rahbani, J.F. / Oppong, A. / Roesler, A. / Kaiser, Z. / Ersin, M. / Zhang, Q. / Guerra Martinez, M. / Shaw, A. / Cheng, J. / Klemets, H. / Illes, K.K. / DeMambro, V.E. / Rosen, C.J. / Millan, J.L. / Wales, T.E. / Langenberg, C. / McKee, M.D. / Guarne, A. / Kazak, L.
History
DepositionFeb 9, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
Revision 1.1May 6, 2026Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alkaline phosphatase, tissue-nonspecific isozyme
B: Alkaline phosphatase, tissue-nonspecific isozyme
C: Alkaline phosphatase, tissue-nonspecific isozyme
D: Alkaline phosphatase, tissue-nonspecific isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,72652
Polymers218,5374
Non-polymers9,18948
Water14,358797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15300 Å2
ΔGint-150 kcal/mol
Surface area33360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.305, 118.893, 346.483
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Alkaline phosphatase, tissue-nonspecific isozyme / AP-TNAP / TNAP / TNSALP / Alkaline phosphatase 2 / Alkaline phosphatase liver/bone/kidney isozyme / ...AP-TNAP / TNAP / TNSALP / Alkaline phosphatase 2 / Alkaline phosphatase liver/bone/kidney isozyme / Phosphoamidase / Phosphocreatine phosphatase


Mass: 54634.262 Da / Num. of mol.: 4 / Mutation: S110A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Alpl, Akp-2, Akp2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P09242, alkaline phosphatase, phosphoamidase

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Sugars , 4 types, 15 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#11: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 9 types, 830 molecules

#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#9: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#10: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#12: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: PO4
#13: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H5O7
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 797 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.12 Å3/Da / Density % sol: 60.64 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.15 M phosphate/citrate pH 4.0, 0.2 M NaCl, 0-30 mM phosphate, 5% glycerol, 14-16% PEG 10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.18 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18 Å / Relative weight: 1
ReflectionResolution: 2.25→39.66 Å / Num. obs: 131060 / % possible obs: 99.68 % / Redundancy: 13.2 % / Biso Wilson estimate: 43.87 Å2 / CC1/2: 0.994 / Rpim(I) all: 0.096 / Net I/σ(I): 6.18
Reflection shellResolution: 2.25→2.33 Å / Num. unique obs: 12937 / CC1/2: 0.345 / Rpim(I) all: 1.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALS3.16.1data reduction
DIALS3.16.1data scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→39.66 Å / SU ML: 0.3496 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.8592
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2318 1943 1.49 %
Rwork0.1903 128737 -
obs0.1909 130680 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.62 Å2
Refinement stepCycle: LAST / Resolution: 2.25→39.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14865 0 568 797 16230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007615776
X-RAY DIFFRACTIONf_angle_d0.930121395
X-RAY DIFFRACTIONf_chiral_restr0.06682432
X-RAY DIFFRACTIONf_plane_restr0.00682746
X-RAY DIFFRACTIONf_dihedral_angle_d14.14075842
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.310.39721400.3728872X-RAY DIFFRACTION97.23
2.31-2.370.33941230.3339086X-RAY DIFFRACTION99.6
2.37-2.440.35461300.39110X-RAY DIFFRACTION99.97
2.44-2.520.3511370.28629096X-RAY DIFFRACTION99.96
2.52-2.610.29811200.26489124X-RAY DIFFRACTION99.98
2.61-2.710.30461540.25099128X-RAY DIFFRACTION99.99
2.71-2.830.2871280.23479186X-RAY DIFFRACTION99.95
2.83-2.980.25191370.21049146X-RAY DIFFRACTION99.97
2.98-3.170.24321360.20239228X-RAY DIFFRACTION99.98
3.17-3.420.27641280.18839193X-RAY DIFFRACTION99.98
3.42-3.760.21191520.16169219X-RAY DIFFRACTION99.97
3.76-4.30.17521510.13689283X-RAY DIFFRACTION99.99
4.3-5.420.1641610.13239389X-RAY DIFFRACTION100
5.42-39.660.20481460.16959677X-RAY DIFFRACTION99.37

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