5B4X Signaling Protein Endocytosis date Apr 20, 2016
title Crystal Structure Of The Apoer2 Ectodomain In Complex With T R56 Fragment
authors N.Yasui, H.Hirai, K.Yamashita, J.Takagi, T.Nogi
compound source
Molecule: Reelin
Chain: A, C
Fragment: Unp Residues 1948-2662
Synonym: Reeler Protein
Ec: 3.4.21.-
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Reln, Rl
Expression_system: Cricetulus Griseus
Expression_system_taxid: 10029

Molecule: Low Density Lipoprotein Receptor-Related Protein Apolipoprotein E Receptor, Isoform Cra_e;
Chain: B, D
Fragment: Apoer2 Ectodomain (Unp Residues 42-607)
Synonym: Lrp-8,Apolipoprotein E Receptor 2
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Lrp8, Hcg_33395
Expression_system: Cricetulus Griseus
Expression_system_taxid: 10029
symmetry Space Group: P 65
R_factor 0.200 R_Free 0.255
length a length b length c angle alpha angle beta angle gamma
205.951 205.951 169.840 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.20 Å
ligand CA, MSE, NAG enzyme Hydrolase E.C.3.4.21 BRENDA
Gene HCG
A, C

D, B

Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (391 Kb) [Save to disk]
  • Biological Unit Coordinates (5b4x.pdb1.gz) 194 Kb
  • Biological Unit Coordinates (5b4x.pdb2.gz) 194 Kb
  • LPC: Ligand-Protein Contacts for 5B4X
  • CSU: Contacts of Structural Units for 5B4X
  • Structure Factors (1434 Kb)
  • Retrieve 5B4X in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5B4X from S2C, [Save to disk]
  • Re-refined 5b4x structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5B4X in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 5B4X
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5b4x from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5b4x] [5b4x_C] [5b4x_D] [5b4x_B] [5b4x_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5B4X
  • Community annotation for 5B4X at PDBWiki (http://pdbwiki.org)

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