9O6J | pdb_00009o6j

Structure of Siglec-10 in complex with 2,3-Sialyllactose

• PDB DOI: https://doi.org/10.2210/pdb9O6J/pdb

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


• Deposited: 2025-04-13 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.39 Å
• R-Value Free: 
  0.292 (Depositor), 0.301 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.268 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

Starting Model: in silico

Literature

Structure of SigLec2,3

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 75.65 kDa 
• Atom Count: 5,287 
• Modeled Residue Count: 653 
• Deposited Residue Count: 657 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sialic acid-binding Ig-like lectin 10	A, B, C [auth D]	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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: Q96LC7-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth C]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-D-glucose	E	2		N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIA (Subject of Investigation/LOI)	H [auth D]	N-acetyl-alpha-neuraminic acid C11 H19 N O9 SQVRNKJHWKZAKO-YRMXFSIDSA-N
NAG	F [auth A], G [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.39 Å
• R-Value Free:  0.292 (Depositor), 0.301 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.268 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.765	α = 90
b = 81.765	β = 90
c = 485.48	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-02-25 
Deposition Author(s): Medina, E., Ming, Q., Tran, T.H., Luca, V.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM133482

Revision History  

• Version 1.0: 2026-02-25
  Type: Initial release