5Y32

Crystal structure of PTP delta Ig1-Ig2 in complex with IL1RAPL1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.701 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Mechanisms of splicing-dependent trans-synaptic adhesion by PTP delta-IL1RAPL1/IL-1RAcP for synaptic differentiation

Yamagata, A.Yoshida, T.Sato, Y.Goto-Ito, S.Uemura, T.Maeda, A.Shiroshima, T.Iwasawa-Okamoto, S.Mori, H.Mishina, M.Fukai, S.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Interleukin-1 receptor accessory protein-like 1
B
346Mus musculusMutation(s): 0 
Gene Names: Il1rapl1
Find proteins for P59823 (Mus musculus)
Go to UniProtKB:  P59823
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Receptor-type tyrosine-protein phosphatase delta
A
305Mus musculusMutation(s): 0 
Gene Names: Ptprd
EC: 3.1.3.48
Find proteins for Q64487 (Mus musculus)
Go to UniProtKB:  Q64487
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUC
Query on FUC

Download SDF File 
Download CCD File 
B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.701 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.214 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 162.975α = 90.00
b = 81.175β = 91.27
c = 91.480γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-07-27 
  • Released Date: 2017-08-16 
  • Deposition Author(s): Yamagata, A., Fukai, S.
  • This entry supersedes: 4YFC

Funding OrganizationLocationGrant Number
JSTJapanCREST

Revision History 

  • Version 1.0: 2017-08-16
    Type: Initial release