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- PDB-9s0v: The Crystal Structure of Human Tissue Nonspecific Alkaline Phosph... -

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Basic information

Entry
Database: PDB / ID: 9s0v
TitleThe Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (hTNAP) in complex with phosphate
ComponentsAlkaline phosphatase, tissue-nonspecific isozyme
KeywordsHYDROLASE / alkaline phosphatase / thermogenesis / structural biology
Function / homology
Function and homology information


phosphoamidase / phosphoamidase activity / phosphoethanolamine phosphatase activity / pyridoxal phosphate metabolic process / response to vitamin B6 / futile creatine cycle / pyridoxal phosphatase activity / developmental process involved in reproduction / ADP phosphatase activity / biomineral tissue development ...phosphoamidase / phosphoamidase activity / phosphoethanolamine phosphatase activity / pyridoxal phosphate metabolic process / response to vitamin B6 / futile creatine cycle / pyridoxal phosphatase activity / developmental process involved in reproduction / ADP phosphatase activity / biomineral tissue development / pyrophosphatase activity / response to macrophage colony-stimulating factor / inhibition of non-skeletal tissue mineralization / cementum mineralization / Post-translational modification: synthesis of GPI-anchored proteins / alkaline phosphatase / alkaline phosphatase activity / response to sodium phosphate / inorganic diphosphate phosphatase activity / phosphate ion homeostasis / endochondral ossification / cellular homeostasis / response to vitamin D / bone mineralization / calcium ion homeostasis / side of membrane / extracellular matrix / response to glucocorticoid / skeletal system development / response to insulin / mitochondrial intermembrane space / mitochondrial membrane / osteoblast differentiation / positive regulation of cold-induced thermogenesis / response to lipopolysaccharide / response to antibiotic / calcium ion binding / ATP hydrolysis activity / extracellular exosome / extracellular region / membrane / 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
PHOSPHATE ION / Alkaline phosphatase, tissue-nonspecific isozyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsBallut, L. / Violot, S. / Imam, I.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: To Be Published
Title: The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (hTNAP) in complex with phosphate
Authors: Ballut, L. / Violot, S. / Imam, I.
History
DepositionJul 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

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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
E: Alkaline phosphatase, tissue-nonspecific isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,63850
Polymers282,2705
Non-polymers9,36845
Water1629
1
A: Alkaline phosphatase, tissue-nonspecific isozyme
B: Alkaline phosphatase, tissue-nonspecific isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,80120
Polymers112,9082
Non-polymers3,89318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12930 Å2
ΔGint-147 kcal/mol
Surface area34110 Å2
MethodPISA
2
C: Alkaline phosphatase, tissue-nonspecific isozyme
hetero molecules

C: Alkaline phosphatase, tissue-nonspecific isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,47720
Polymers112,9082
Non-polymers3,56918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area12580 Å2
ΔGint-146 kcal/mol
Surface area33990 Å2
MethodPISA
3
D: Alkaline phosphatase, tissue-nonspecific isozyme
E: Alkaline phosphatase, tissue-nonspecific isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,59820
Polymers112,9082
Non-polymers3,69018
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12870 Å2
ΔGint-163 kcal/mol
Surface area34330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.730, 297.700, 205.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 5 molecules ABCDE

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


Mass: 56453.965 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALPL / Plasmid: pcDNA3.4 / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
References: UniProt: P05186, alkaline phosphatase, phosphoamidase

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Sugars , 3 types, 20 molecules

#2: 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.: 10
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
#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.: 4
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
#7: 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: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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 , 5 types, 34 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 4.24 Å3/Da / Density % sol: 71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium phosphate, 20% (w/v) PEG 3350 / PH range: 6.5 - 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 16, 2025
RadiationMonochromator: horizontally diffraction Si (111) monochromator, compound refractive lenses (CRLs), half-Kirkpatrick-Baez (KB)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 3.35→39.56 Å / Num. obs: 69299 / % possible obs: 99.2 % / Redundancy: 14 % / Biso Wilson estimate: 71.39 Å2 / CC1/2: 0.992 / Rrim(I) all: 0.4 / Net I/σ(I): 7.25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2% possible allRrim(I) all
3.35-3.5512.22.17107530.39996.6
3.55-3.814.83.13104620.673100
3.8-4.114.93.8997530.8281000.951
4.1-4.4914.65.9290050.9471000.584
4.49-5.0114.57.4581720.9740.425
5.01-5.78146.7672270.9799.60.458
5.78-7.0512.58.9961160.98299.20.32
5.78-7.0514.748150.997990.133
7.05-9.8813.728690.99998.60.079

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHASER2.8.3phasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.35→39.56 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2656 3438 5 %Random slection
Rwork0.2153 ---
obs0.2178 68720 99.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.35→39.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18656 0 565 9 19230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00419625
X-RAY DIFFRACTIONf_angle_d0.94426630
X-RAY DIFFRACTIONf_dihedral_angle_d15.8277741
X-RAY DIFFRACTIONf_chiral_restr0.0773011
X-RAY DIFFRACTIONf_plane_restr0.0063444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.35-3.40.41141360.39492569X-RAY DIFFRACTION100
3.4-3.450.37451360.35642594X-RAY DIFFRACTION100
3.45-3.50.37621350.33352568X-RAY DIFFRACTION100
3.5-3.550.37831380.31882614X-RAY DIFFRACTION100
3.55-3.610.40961350.31322570X-RAY DIFFRACTION100
3.61-3.670.32391380.3012619X-RAY DIFFRACTION100
3.67-3.740.35371380.28462609X-RAY DIFFRACTION100
3.74-3.810.30571350.27582575X-RAY DIFFRACTION100
3.81-3.890.35571370.26352595X-RAY DIFFRACTION100
3.89-3.970.34231370.24212606X-RAY DIFFRACTION100
3.97-4.070.25041370.21042600X-RAY DIFFRACTION100
4.07-4.170.23721370.19652605X-RAY DIFFRACTION100
4.17-4.280.22741370.18242612X-RAY DIFFRACTION100
4.28-4.410.22811370.17492590X-RAY DIFFRACTION100
4.41-4.550.21851380.16692619X-RAY DIFFRACTION100
4.55-4.710.23311350.15972599X-RAY DIFFRACTION100
4.71-4.90.20741380.16382618X-RAY DIFFRACTION100
4.9-5.120.24241380.16912624X-RAY DIFFRACTION100
5.12-5.390.22321390.18692625X-RAY DIFFRACTION100
5.39-5.730.26671360.18772590X-RAY DIFFRACTION99
5.73-6.170.24211390.17722633X-RAY DIFFRACTION99
6.17-6.790.23191380.18982625X-RAY DIFFRACTION99
6.79-7.760.20111380.15822618X-RAY DIFFRACTION99
7.76-9.750.19231400.1482671X-RAY DIFFRACTION99
8-100.23091460.2132734X-RAY DIFFRACTION98

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