9JDO | pdb_00009jdo

LCN2 in complex with phosphoserine

PDB DOI: https://doi.org/10.2210/pdb9JDO/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-08-31 Released: 2025-09-03
Deposition Author(s): Qin, J., Hu, X., Wang, L., Wei, H.
Funding Organization(s): Chinese Academy of Sciences

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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Ligand Structure Quality Assessment

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Literature

Targeting LCN2 breaks the phosphatidylserine-rich niches to restore NK cells anti-tumor immunity

Qin, J., Hu, X., Wang, L., Wei, H.

To be published.

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:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutrophil gelatinase-associated lipocalin	A	178	Homo sapiens	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80188
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SEP (Subject of Investigation/LOI) Query on SEP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PHOSPHOSERINE C₃ H₈ N O₆ P BZQFBWGGLXLEPQ-REOHCLBHSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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 = 53.107	α = 90
b = 53.107	β = 90
c = 126.244	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	--

Revision History (Full details and data files)

Version 1.0: 2025-09-03
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.