5B4X

Crystal structure of the ApoER2 ectodomain in complex with the Reelin R56 fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of the ectodomain from a LDLR close homologue in complex with its physiological ligand.

Hirai, H.Yasui, N.Yamashita, K.Tabata, S.Yamamoto, M.Takagi, J.Nogi, T.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Reelin
A, C
725Mus musculusMutation(s): 1 
Gene Names: Reln (Rl)
EC: 3.4.21.-
Find proteins for Q60841 (Mus musculus)
Go to UniProtKB:  Q60841
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Low density lipoprotein receptor-related protein 8, apolipoprotein e receptor, isoform CRA_e
B, D
570Homo sapiensMutation(s): 0 
Gene Names: LRP8 (APOER2)
Find proteins for Q14114 (Homo sapiens)
Go to Gene View: LRP8
Go to UniProtKB:  Q14114
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.200 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 205.951α = 90.00
b = 205.951β = 90.00
c = 169.840γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
autoSHARPphasing
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPSJapan22247010
JSPSJapan20770084
JSPSJapan05J09821
MEXTJapan17082004

Revision History 

  • Version 1.0: 2017-04-26
    Type: Initial release