2FYL	Surface Active Protein	date	Feb 08, 2006
title	Haddock Model Of The Complex Between Double Module Of Lrp, Cr56, And First Domain Of Receptor Associated Protein, Rap- D1.
authors	G.A.Jensen, O.M.Andersen, A.M.Bonvin, I.Bjerrum-Bohr, M.Etzerodt, C.O'Shea, F.M.Poulsen, B.B.Kragelund
compound		source
Molecule: Alpha-2-Macroglobulin Receptor-Associated Protein; Chain: A Fragment: Rapd1 Synonym: Alpha-2- Mrap, Low Density Lipoprotein Receptor- Related Protein-Associated Protein 1, Rap; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Lrpap1, A2mrap Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: Low-Density Lipoprotein Receptor-Related Protein 1; Chain: B Fragment: Cr56 Synonym: Lrp, Alpha-2-Macroglobulin Receptor Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Lrp1 Expression_system: Escherichia Coli Expression_system_taxid: 562
method	Solution NMR
ligand	CA	enzyme
Gene Ontology	Chain Function Process Component A asialoglycoprotein receptor ... heparin binding lipase binding receptor antagonist activity... low-density lipoprotein part... unfolded protein binding very-low-density lipoprotein... protein folding negative regulation of very-... vesicle-mediated transport negative regulation of prote... extracellular negative regul... negative regulation of beta-... extracellular region cytoplasm endoplasmic reticulum plasma membrane cell surface integral to membrane vesicle rough endoplasmic reticulum ...
Primary reference	Binding Site Structure of One LRP-RAP Complex:Implications for a Common Ligand-Receptor Binding Motif., Jensen GA, Andersen OM, Bonvin AM, Bjerrum-Bohr I, Etzerodt M, Thogersen HC, O'shea C, Poulsen FM, Kragelund BB, J Mol Biol. 2006 Sep 29;362(4):700-16. Epub 2006 Jul 15. PMID:16938309

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (51 Kb) [Save to disk] LPC: Ligand-Protein Contacts for 2FYL CSU: Contacts of Structural Units for 2FYL Original NMR restraints for 2FYL from PDB Retrieve 2FYL in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2FYL from S2C, [Save to disk]

View 2FYL 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 2FYL

Cartoon representation from PDB Cartoon Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 2FYL, from MSDmotif at EBI Fold representative 2fyl from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2fyl_A] [2fyl_B] SWISS-PROT database: [P30533] [Q07954] Domain organization of [AMRP_HUMAN] [LRP1_HUMAN] by SWISSPFAM Domain found in 2FYL: [LDLa ] by SMART Alignments of the sequence of 2FYL with the sequences similar proteins can be viewed for 2FYL's classification [AMRP_HUMAN] [LRP1_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [AMRP_HUMAN] [LRP1_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 2FYL

Community annotation for 2FYL at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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