9O6N | pdb_00009o6n

Structure of Siglec-10

PDB DOI: https://doi.org/10.2210/pdb9O6N/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2025-04-14 Released: 2026-02-25
Deposition Author(s): Medina, E., Ming, Q., Tran, T.H., Luca, V.C.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.98 Å
R-Value Free:
0.259 (Depositor), 0.259 (DCC)
R-Value Work:
0.212 (Depositor), 0.218 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: in silico
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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

Structure of apo-SigLec10

Medina, E., Ming, Q., Tran, T.H., Luca, V.C.

To be published.

Macromolecule Content

Total Structure Weight: 75.72 kDa
Atom Count: 5,296
Modeled Residue Count: 654
Deposited Residue Count: 657
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sialic acid-binding Ig-like lectin 10	A, B, C	219	Homo sapiens	Mutation(s): 0 Gene Names: SIGLEC10, SLG2, UNQ477/PRO940
UniProt & NIH Common Fund Data Resources
Find proteins for Q96LC7 (Homo sapiens) Explore Q96LC7 Go to UniProtKB: Q96LC7
PHAROS: Q96LC7 GTEx: ENSG00000142512
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96LC7
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B	Go to GlyGen: Q96LC7-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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	D	3		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 4 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 G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
FLC (Subject of Investigation/LOI) Query on FLC Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth C] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth C] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain J [auth C] mmCIF format, chain E [auth A]	E [auth A], F [auth A], J [auth C]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B]	H [auth B], K [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain K [auth C] Interactions & Density Focus chain H [auth B] Focus chain K [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]