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 9JDO | pdb_00009jdo

LCN2 in complex with phosphoserine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.286 (Depositor), 0.277 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.236 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 

Literature

Inhibition of the lipocalin-2-phosphatidylserine axis restores natural killer cell immune surveillance.

Qin, J., Hu, X., Wang, L., Cai, Y., Hu, Z., Xu, X., Nian, Z., Liu, Z., Ding, X., Jiang, Y., Lin, Y., Ruan, K., Fu, B., Tian, Z., Zhou, Y., Wei, H.

(2026) Cell Rep Med : 103012-103012

  • DOI: https://doi.org/10.1016/j.xcrm.2026.103012
  • Primary Citation Related Structures: 
    9JDO

  • PubMed Abstract: 

    Lipid metabolic reprogramming can facilitate immune escape by promoting a suppressive phenotype in tumor-infiltrating immune cells, although this process remains poorly understood. Here, we identify the lipoprotein, Lipocalin-2 (LCN2), as an essential factor driving natural killer (NK) cell dysfunction and immunosuppressive phenotype. Spatial metabolomics with crystal structure analysis demonstrates that LCN2 binding to phosphatidylserine (PS) and PS enrichment is required for tumor-associated lipid reprogramming. Increased LCN2-PS binding limits IL-15-mediated JAK-STAT pathway activation in NK cells, while inhibiting tumor-infiltrating neutrophil maintenance of anti-tumor potential in NK cells via suppression of IFN-I response. Structure-based drug screening identifies semapimod as an LCN2 inhibitor that blocks interaction with PS, disrupting the LCN2-PS immunosuppressive axis and inducing tumor control. Overall, this study uncovers a lipid metabolic reprogramming mechanism that mediates innate immune evasion and proposes a tumor treatment strategy through enhanced innate immune surveillance.


  • Organizational Affiliation: 
    • National Key Laboratory of Immune Response and Immunotherapy, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China; Institute of Immunology, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China.

Macromolecule Content 

  • Total Structure Weight: 20.76 kDa 
  • Atom Count: 1,380 
  • Modeled Residue Count: 173 
  • Deposited Residue Count: 178 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Neutrophil gelatinase-associated lipocalin178Homo sapiensMutation(s): 0 
Gene Names: LCN2, HNL, NGAL
UniProt & NIH Common Fund Data Resources
Find proteins for P80188 (Homo sapiens)
Explore P80188 
Go to UniProtKB:  P80188
PHAROS:  P80188
GTEx:  ENSG00000148346 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80188
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SEP
(Subject of Investigation/LOI)

Query on SEP



Download:Ideal Coordinates CCD File
B [auth A]PHOSPHOSERINE
C3 H8 N O6 P
BZQFBWGGLXLEPQ-REOHCLBHSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.286 (Depositor), 0.277 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 0.236 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.107α = 90
b = 53.107β = 90
c = 126.244γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChina--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release
  • Version 1.1: 2026-09-23
    Changes: Database references