9S0V | pdb_00009s0v

The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (hTNAP) in complex with phosphate

PDB DOI: https://doi.org/10.2210/pdb9S0V/pdb

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

Deposited: 2025-07-17 Released: 2025-09-17
Deposition Author(s): Ballut, L., Violot, S., Imam, I.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.35 Å
R-Value Free:
0.266 (Depositor), 0.266 (DCC)
R-Value Work:
0.215 (Depositor), 0.215 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The Crystal Structure of Human Tissue Nonspecific Alkaline Phosphatase (hTNAP) in complex with phosphate

Ballut, L., Violot, S., Imam, I.

To be published.

Macromolecule Content

Total Structure Weight: 291.64 kDa
Atom Count: 19,230
Modeled Residue Count: 2,411
Deposited Residue Count: 2,545
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alkaline phosphatase, tissue-nonspecific isozyme	A, B, C, D, E	509	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: 4	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E	Go to GlyGen: P05186-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, G, I, J, L F, G, I, J, L, M, N, O, P, R	2		N-Glycosylation	Interactions Focus chain F Focus chain G Focus chain I Focus chain J Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain R Interactions & Density Focus chain F Focus chain G Focus chain I Focus chain J Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain R
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
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	H, K, Q, S	3		N-Glycosylation	Interactions Focus chain H Focus chain K Focus chain Q Focus chain S Interactions & Density Focus chain H Focus chain K Focus chain Q Focus chain S
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain JA [auth C] SDF format, chain PA [auth D] SDF format, chain VA [auth E] SDF format, chain WA [auth E] SDF format, chain X [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain JA [auth C] MOL2 format, chain PA [auth D] MOL2 format, chain VA [auth E] MOL2 format, chain WA [auth E] MOL2 format, chain X [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain JA [auth C] mmCIF format, chain PA [auth D] mmCIF format, chain VA [auth E] mmCIF format, chain WA [auth E] mmCIF format, chain X [auth A]	DA [auth B] JA [auth C] PA [auth D] VA [auth E] WA [auth E] DA [auth B], JA [auth C], PA [auth D], VA [auth E], WA [auth E], X [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain DA [auth B] Focus chain JA [auth C] Focus chain PA [auth D] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain X [auth A] Interactions & Density Focus chain DA [auth B] Focus chain JA [auth C] Focus chain PA [auth D] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain X [auth A]
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain KA [auth C] SDF format, chain QA [auth D] SDF format, chain XA [auth E] SDF format, chain Y [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain KA [auth C] MOL2 format, chain QA [auth D] MOL2 format, chain XA [auth E] MOL2 format, chain Y [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain KA [auth C] mmCIF format, chain QA [auth D] mmCIF format, chain XA [auth E] mmCIF format, chain Y [auth A]	EA [auth B], KA [auth C], QA [auth D], XA [auth E], Y [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain EA [auth B] Focus chain KA [auth C] Focus chain QA [auth D] Focus chain XA [auth E] Focus chain Y [auth A] Interactions & Density Focus chain EA [auth B] Focus chain KA [auth C] Focus chain QA [auth D] Focus chain XA [auth E] Focus chain Y [auth A]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain RA [auth E] SDF format, chain SA [auth E] SDF format, chain U [auth A] SDF format, chain Z [auth B] SDF format, chain T [auth A] SDF format, chain AA [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain RA [auth E] MOL2 format, chain SA [auth E] MOL2 format, chain U [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain T [auth A] MOL2 format, chain AA [auth B] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain LA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain RA [auth E] mmCIF format, chain SA [auth E] mmCIF format, chain U [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain T [auth A] mmCIF format, chain AA [auth B]	AA [auth B] FA [auth C] GA [auth C] LA [auth D] MA [auth D] AA [auth B], FA [auth C], GA [auth C], LA [auth D], MA [auth D], RA [auth E], SA [auth E], T [auth A], U [auth A], Z [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain T [auth A] Focus chain U [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain T [auth A] Focus chain U [auth A] Focus chain Z [auth B]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain OA [auth D] SDF format, chain UA [auth E] SDF format, chain W [auth A] SDF format, chain IA [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain OA [auth D] MOL2 format, chain UA [auth E] MOL2 format, chain W [auth A] MOL2 format, chain IA [auth C] mmCIF format, chain CA [auth B] mmCIF format, chain OA [auth D] mmCIF format, chain UA [auth E] mmCIF format, chain W [auth A] mmCIF format, chain IA [auth C]	CA [auth B], IA [auth C], OA [auth D], UA [auth E], W [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain IA [auth C] Focus chain OA [auth D] Focus chain UA [auth E] Focus chain W [auth A] Interactions & Density Focus chain CA [auth B] Focus chain IA [auth C] Focus chain OA [auth D] Focus chain UA [auth E] Focus chain W [auth A]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain HA [auth C] SDF format, chain TA [auth E] SDF format, chain V [auth A] SDF format, chain NA [auth D] SDF format, chain BA [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain TA [auth E] MOL2 format, chain V [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain BA [auth B] mmCIF format, chain HA [auth C] mmCIF format, chain TA [auth E] mmCIF format, chain V [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain BA [auth B]	BA [auth B], HA [auth C], NA [auth D], TA [auth E], V [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain HA [auth C] Focus chain NA [auth D] Focus chain TA [auth E] Focus chain V [auth A] Interactions & Density Focus chain BA [auth B] Focus chain HA [auth C] Focus chain NA [auth D] Focus chain TA [auth E] Focus chain V [auth A]