13EW | pdb_000013ew

Netrin-1 with heparin oligosaccharide ligand

• PDB DOI: https://doi.org/10.2210/pdb13EW/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Gallus gallus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2026-05-04 Released: 2026-10-14 
• Deposition Author(s): Meier, M., Moya-Torres, A., Gupta, M., McDougall, M.D., Bailey-Elkin, B.A., Koch, M., Stetefeld, J.
• Funding Organization(s): German Research Foundation (DFG), Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.08 Å
• R-Value Free: 
  0.220 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.194 (DCC) 

Starting Model: experimental

Literature

Netrin-1 with heparin oligosaccharide ligand

Meier, M., Stetefeld, J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 57.84 kDa 
• Atom Count: 3,835 
• Modeled Residue Count: 420 
• Deposited Residue Count: 443 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Netrin-1	A	443	Gallus gallus	Mutation(s): 0  Gene Names: NTN1
UniProt
Find proteins for Q90922 (Gallus gallus) Explore Q90922  Go to UniProtKB:  Q90922
Glycosylation
Glycosylation Sites: 4

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B [auth N]	7		N-Glycosylation
Glycosylation Resources
GlyTouCan: G69411IG GlyCosmos: G69411IG GlyGen: G69411IG

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth O]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth P]	6		N-Glycosylation
Glycosylation Resources
GlyTouCan: G82348BZ GlyCosmos: G82348BZ GlyGen: G82348BZ

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth Q]	6		N-Glycosylation
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose	F [auth H]	14		N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.08 Å
• R-Value Free:  0.220 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.194 (DCC) 

Diffraction Data: https://doi.org/10.18430/M313EW

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 204.774	α = 90
b = 204.774	β = 90
c = 99.233	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
JBluIce-EPICS	data collection
XDS	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building
STARANISO	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-14 
Deposition Author(s): Meier, M., Moya-Torres, A., Gupta, M., McDougall, M.D., Bailey-Elkin, B.A., Koch, M., Stetefeld, J.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	DFG-FOR2722
Canadian Institutes of Health Research (CIHR)	Canada	CIHR-PJT 152935

Revision History  

• Version 1.0: 2026-10-14
  Type: Initial release
  
• Version 1.1: 2026-10-21
  Changes: Database references