9SH5 | pdb_00009sh5

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

PDB DOI: https://doi.org/10.2210/pdb9SH5/pdb
EM Map EMD-54888: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-08-25 Released: 2025-11-05
Deposition Author(s): Imam, I., Coureux, P.D., Ballut, L.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.27 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9SH5

This is version 1.0 of the entry. See complete history.

Literature

TNAP dephosphorylates phosphocholine and phosphoethanolamine and participates in triglyceride transport from the liver to the bloodstream

Drevet Mulard, E., Imam, I., Coureux, P.D., Briolay, A., Bessueille, L., Tarby, A., Balayssac, S., Narisawa, S., Lecornu, F., Gilard, V., Violot, S., Millan, J.L., Rautureau, G.J.P., Ballut, L., Magne, D.

To be published.

Macromolecule Content

Total Structure Weight: 119.95 kDa
Atom Count: 7,890
Modeled Residue Count: 964
Deposited Residue Count: 1,024
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alkaline phosphatase, tissue-nonspecific isozyme	A, B	512	Homo sapiens	Mutation(s): 0 Gene Names: ALPL EC: 3.1.3.1 (PDB Primary Data), 3.9.1.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P05186 (Homo sapiens) Explore P05186 Go to UniProtKB: P05186
PHAROS: P05186 GTEx: ENSG00000162551
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05186
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain A Focus chain B	Go to GlyGen: P05186-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, L	3		N-Glycosylation	Interactions Focus chain C Focus chain L Interactions & Density Focus chain C Focus chain L
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E, I, K	2		N-Glycosylation	Interactions Focus chain D Focus chain E Focus chain I Focus chain K Interactions & Density Focus chain D Focus chain E Focus chain I Focus chain K
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, J	2		N-Glycosylation	Interactions Focus chain F Focus chain J Interactions & Density Focus chain F Focus chain J
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	G, H	5		N-Glycosylation	Interactions Focus chain G Focus chain H Interactions & Density Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G42466VF GlyCosmos: G42466VF GlyGen: G42466VF

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JNY (Subject of Investigation/LOI) Query on A1JNY Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain V [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain V [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain V [auth B]	Q [auth A], V [auth B]	2,5-dimethoxy-~{N}-quinolin-3-yl-benzenesulfonamide C₁₇ H₁₆ N₂ O₄ S JZSPHTPWUXNQGB-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Focus chain V [auth B] Interactions & Density Focus chain Q [auth A] Focus chain V [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain P [auth A] SDF format, chain S [auth B] SDF format, chain U [auth B] MOL2 format, chain N [auth A] MOL2 format, chain P [auth A] MOL2 format, chain S [auth B] MOL2 format, chain U [auth B] mmCIF format, chain N [auth A] mmCIF format, chain P [auth A] mmCIF format, chain S [auth B] mmCIF format, chain U [auth B]	N [auth A], P [auth A], S [auth B], U [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain P [auth A] Focus chain S [auth B] Focus chain U [auth B] Interactions & Density Focus chain N [auth A] Focus chain P [auth A] Focus chain S [auth B] Focus chain U [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain T [auth B] MOL2 format, chain O [auth A] MOL2 format, chain T [auth B] mmCIF format, chain O [auth A] mmCIF format, chain T [auth B]	O [auth A], T [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain T [auth B] Interactions & Density Focus chain O [auth A] Focus chain T [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain R [auth B] MOL2 format, chain M [auth A] MOL2 format, chain R [auth B] mmCIF format, chain M [auth A] mmCIF format, chain R [auth B]	M [auth A], R [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain R [auth B] Interactions & Density Focus chain M [auth A] Focus chain R [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.27 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419:
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-23-CE44-0036

Revision History (Full details and data files)

Version 1.0: 2025-11-05
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.