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- PDB-10ty: Tissue Non-specific Alkaline Phosphatase -S110A bound to PPi with... -

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Basic information

Entry
Database: PDB / ID: 10ty
TitleTissue Non-specific Alkaline Phosphatase -S110A bound to PPi with ethylene glycol
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 / alpha-D-mannopyranose / PHOSPHATE ION / PYROPHOSPHATE 2- / Alkaline phosphatase, tissue-nonspecific isozyme
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 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)228,13546
Polymers218,5374
Non-polymers9,59842
Water13,421745
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15020 Å2
ΔGint-130 kcal/mol
Surface area34780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.270, 118.676, 346.968
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 , 7 types, 19 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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: 894.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 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-L-Fucp]{}}LINUCSPDB-CARE
#3: 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)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_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]{}}}}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.: 4
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
#5: 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
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#12: 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.: 9 / Source method: obtained synthetically / 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
#13: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 8 types, 768 molecules

#7: Chemical
ChemComp-POP / PYROPHOSPHATE 2-


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


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


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


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#11: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#14: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#15: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 745 / 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: 60.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.15 M phosphate/citrate pH 4.0, 0.2 M NaCl, 0-30 mM phosphate, 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18 Å / Relative weight: 1
ReflectionResolution: 2.28→39.69 Å / Num. obs: 125850 / % possible obs: 99.21 % / Redundancy: 13.2 % / Biso Wilson estimate: 40.82 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.1 / Net I/σ(I): 4.44
Reflection shellResolution: 2.28→2.34 Å / Num. unique obs: 12396 / CC1/2: 0.34 / Rpim(I) all: 1.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALS3.16.1data reduction
DIALS3.16.1data scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→39.69 Å / SU ML: 0.3973 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.7367
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2494 1972 1.58 %
Rwork0.211 122935 -
obs0.2116 124907 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.55 Å2
Refinement stepCycle: LAST / Resolution: 2.28→39.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14890 0 594 745 16229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003315805
X-RAY DIFFRACTIONf_angle_d0.566521439
X-RAY DIFFRACTIONf_chiral_restr0.04852462
X-RAY DIFFRACTIONf_plane_restr0.00622742
X-RAY DIFFRACTIONf_dihedral_angle_d12.90965866
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.340.38011140.38118007X-RAY DIFFRACTION91.86
2.34-2.40.40121190.3588617X-RAY DIFFRACTION98.69
2.4-2.470.39671560.33728776X-RAY DIFFRACTION99.91
2.47-2.550.34011340.32018745X-RAY DIFFRACTION99.94
2.55-2.640.36551370.28698763X-RAY DIFFRACTION99.96
2.64-2.750.29431430.2788728X-RAY DIFFRACTION99.95
2.75-2.870.28151340.25248801X-RAY DIFFRACTION99.87
2.87-3.020.29691490.23868802X-RAY DIFFRACTION99.98
3.02-3.210.24961590.2218770X-RAY DIFFRACTION99.98
3.21-3.460.28051470.20168829X-RAY DIFFRACTION99.94
3.46-3.810.20791470.16988850X-RAY DIFFRACTION99.98
3.81-4.360.15981250.14328967X-RAY DIFFRACTION99.99
4.36-5.490.16991340.14999024X-RAY DIFFRACTION100
5.49-39.690.23531740.19449256X-RAY DIFFRACTION99.22

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