5GJE	Signaling Protein	date	Jun 29, 2016
title	Three-Dimensional Reconstruction Of Human Lrp6 Ectodomain Co With Dkk1
authors	K.Matoba, E.Mihara, K.Tamura-Kawakami, H.Hirai, S.Thompson, K.Iwa J.Takagi
compound		source
Molecule: Low-Density Lipoprotein Receptor-Related Protein Chain: A Fragment: Unp Residues 20-630 Synonym: Lrp-6 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Lrp6 Expression_system: Cricetulus Griseus Expression_system_taxid: 10029 Expression_system_vector_type: Plasmid
Molecule: Low-Density Lipoprotein Receptor-Related Protein Chain: B Fragment: Unp Residues 631-1246 Synonym: Lrp-6 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Lrp6 Expression_system: Spodoptera Frugiperda Expression_system_taxid: 7108
Molecule: Dickkopf-Related Protein 1 Chain: C Synonym: Hdkk-1,Sk Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Dkk1, Unq492pro1008 Expression_system: Spodoptera Frugiperda Expression_system_taxid: 7108
symmetry	Space Group: P 1	R_factor R_Free
crystal cell	length a length b length c angle alpha angle beta angle gamma 1.000 1.000 1.000 90.00 90.00 90.00
method	Electron Microscopy	resolution	21.00 Å
ligand	FUC, GOL, NAG, PO4	enzyme
Primary reference	Conformational Freedom of the LRP6 Ectodomain Is Regulated by N-glycosylation and the Binding of the Wnt Antagonist Dkk1., Matoba K, Mihara E, Tamura-Kawakami K, Miyazaki N, Maeda S, Hirai H, Thompson S, Iwasaki K, Takagi J, Cell Rep. 2017 Jan 3;18(1):32-40. doi: 10.1016/j.celrep.2016.12.017. PMID:28052259

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (329 Kb) [Save to disk] Biological Unit Coordinates (5gje.pdb1.gz) 324 Kb LPC: Ligand-Protein Contacts for 5GJE CSU: Contacts of Structural Units for 5GJE Retrieve 5GJE in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5GJE from S2C, [Save to disk]

View 5GJE 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 5GJE

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5gje_C] [5gje_A] [5gje] [5gje_B] SWISS-PROT database: Domain organization of by SWISSPFAM

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