5XWU

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Receptor-type tyrosine-protein phosphatase delta
A, C
313Mus musculusMutation(s): 0 
Gene Names: Ptprd
EC: 3.1.3.48
Find proteins for Q64487 (Mus musculus)
Go to UniProtKB:  Q64487
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Leucine-rich repeat and fibronectin type III domain-containing protein 1
B, D
365Mus musculusMutation(s): 0 
Gene Names: Lrfn1 (Salm2, Semo1)
Find proteins for Q2WF71 (Mus musculus)
Go to UniProtKB:  Q2WF71
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
A, C
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
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 = 90.040α = 90.00
b = 127.198β = 90.00
c = 210.919γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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