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9sh5

The cryo-EM structure of human Tissue Nonspecific Alkaline Phosphatase (hTNAP) in complex with MLS-0038949

Method: ELECTRON MICROSCOPY D_max: 102.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sh5
deposition_date	2025-08-25
title	The cryo-EM structure of human Tissue Nonspecific Alkaline Phosphatase (hTNAP) in complex with MLS-0038949
keywords	Inhibitor, Alkaline Phosphatase, HYDROLASE; HYDROLASE
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	30.87 Å
rg_electron	30.32 Å
i0	395780000.00
molecular_weight	104880.0 kDa
excluded_volume	100330 Å³
envelope_volume	172500 Å³
shell_volume	46008 Å³
envelope_diameter	112.4 Å
shell_rg	38.65 Å
envelope_rg	30.79 Å
shape_rg	30.27 Å
total_rg	30.86 Å
total_atoms	7922
n_residues	964
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	102.5 Å
rg_real	30.85 Å
rg_real_error	0.70 Å
i0_real	3.9580e+08
i0_real_error	5.7190e+06
rg_reciprocal	30.86 Å
i0_reciprocal	395800000.0000
total_estimate	0.8775
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	36.2 Å
skewness	0.391
kurtosis	-0.195
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	63110000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.818; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.952

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 polymer

description	Alkaline phosphatase, tissue-nonspecific isozyme
formula_weight	56739.3 kDa
ec_number	3.1.3.1,3.9.1.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	7922

GRALVPEKEKDPKYWRDQAQETLKYALELQKLNTNVAKNVIMFLGDGMGVSTVTAARILKGQLHHNPGEETRLEMDKFPFVALSKTYNTNAQVPDSAGTATAYLCGVKANEGTVGVSAATERSRCNTTQGNEVTSILRWAKDAGKSVGIVTTTRVNHATPSAAYAHSADRDWYSDNEMPPEALSQGCKDIAYQLMHNIRDIDVIMGGGRKYMYPKNKTDVEYESDEKARGTRLDGLDLVDTWKSFKPRYKHSHFIWNRTELLTLDPHNVDYLLGLFEPGDMQYELNRNNVTDPSLSEMVVVAIQILRKNPKGFFLLVEGGRIDHGHHEGKAKQALHEAVEMDRAIGQAGSLTSSEDTLTVVTADHSHVFTFGGYTPRGNSIFGLAPMLSDTDKKPFTAILYGNGPGYKVVGGERENVSMVDYAHNNYQAQSAVPLRHETHGGEDVAVFSKGPMAHLLHGVHEQNYVPHVMAYAACIGANLGHCAPAAAAENLYFQGDYKDDDDKHHHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 branched

description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	586.5 kDa
src_method	man
entity_count	2

Entity 3 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	4

Entity 4 branched

description	alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	367.3 kDa
src_method	man
entity_count	2

Entity 5 branched

description	;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 ;
formula_weight	894.8 kDa
src_method	man
entity_count	2

Entity 6 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	4

Entity 8 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

Entity 9 non-polymer

description	2,5-dimethoxy-~{N}-quinolin-3-yl-benzenesulfonamide
formula_weight	344.4 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.27 Å
resolution_method	—
num_particles	465956

fit	/app/data/saxs_computation/sh/9sh5/9sh5.fit
pddf	/app/data/pr_computation/sh/9sh5/9sh5.pr.out
profile	/app/data/saxs_computation/sh/9sh5/9sh5.dat