Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content

• Total Structure Weight: 151978.39 
• Atom Count: 9973 
• Residue Count: 1356 
• Unique protein chains: 2

5XWU

Crystal structure of PTPdelta Ig1-Ig3 in complex with SALM2 LRR-Ig

• DOI: 10.2210/pdb5XWU/pdb

• Classification: CELL ADHESION
• Organism(s): Mus musculus
• Expression System: Homo sapiens


• Deposited: 2017-06-30 Released: 2018-06-06 
• Deposition Author(s): Goto-Ito, S., Yamagata, A., Sato, Y., Fukai, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.162 Å
• R-Value Free: 0.259 
• R-Value Work: 0.218 

Literature

Structural basis of trans-synaptic interactions between PTP delta and SALMs for inducing synapse formation.

Goto-Ito, S., Yamagata, A., Sato, Y., Uemura, T., Shiroshima, T., Maeda, A., Imai, A., Mori, H., Yoshida, T., Fukai, S.

(2018) Nat Commun 9: 269-269

• PubMed: 29348429 
• Primary Citation of Related Structures:  
  5XWT, 5XWS

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Receptor-type tyrosine-protein phosphatase delta	A, C	313	Mus musculus	Mutation(s): 0  Gene Names: Ptprd EC: 3.1.3.48
Find proteins for Q64487 (Mus musculus) Go to UniProtKB:  Q64487

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Leucine-rich repeat and fibronectin type III domain-containing protein 1	B, D	365	Mus musculus	Mutation(s): 0  Gene Names: Lrfn1 (Salm2, Semo1)
Find proteins for Q2WF71 (Mus musculus) Go to UniProtKB:  Q2WF71

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NAG	A, B, C, D	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MES	A, C	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.162 Å
• R-Value Free: 0.259 
• R-Value Work: 0.218 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 90.040	α = 90.00
b = 127.198	β = 90.00
c = 210.919	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	refinement
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-06-30 
• Released Date: 2018-06-06 
• Deposition Author(s): Goto-Ito, S., Yamagata, A., Sato, Y., Fukai, S.

Revision History 

• Version 1.0: 2018-06-06
  Type: Initial release