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
methodSolution NMR
ligand CA enzyme
Primary referenceBinding 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.
  • 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_B] [2fyl_A] [2fyl]
  • 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)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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