1F5Y Lipid Binding Protein date Jun 18, 2000
title Nmr Structure Of A Concatemer Of The First And Second Ligand Modules Of The Human Ldl Receptor
authors N.D.Kurniawan, A.R.Atkins, I.M.Brereton, P.A.Kroon, R.Smith
compound source
Molecule: Low-Density Lipoprotein Receptor
Chain: A
Fragment: Ligand-Binding Modules 1-2
Synonym: Ldl Receptor
Engineered: Yes
Other_details: Ligand-Binding Module Concatemer
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Liver
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector: Pgex-2t, Gst-Fusion Protein
methodSolution NMR
ligand CA enzyme
related structures by homologous chain: 1LDL, 1LDR
Primary referenceNMR structure of a concatemer of the first and second ligand-binding modules of the human low-density lipoprotein receptor., Kurniawan ND, Atkins AR, Bieri S, Brown CJ, Brereton IM, Kroon PA, Smith R, Protein Sci 2000 Jul;9(7):1282-93. PMID:10933493
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (404 Kb) [Save to disk]
  • Biological Unit Coordinates (1f5y.pdb1.gz) 21 Kb
  • LPC: Ligand-Protein Contacts for 1F5Y
  • CSU: Contacts of Structural Units for 1F5Y
  • Original NMR restraints for 1F5Y from PDB
  • Retrieve 1F5Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1F5Y from S2C, [Save to disk]
    • View 1F5Y 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 1F5Y
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1F5Y, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1f5ya1, region A:1-44 [Jmol] [rasmolscript] [script source]
        - Domain d1f5ya2, region A:45-85 [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1f5y] [1f5y_A]
  • SWISS-PROT database: [P01130]
  • Domain organization of [LDLR_HUMAN] by SWISSPFAM
  • Domain found in 1F5Y: [LDLa ] by SMART
    • Other resources with information on 1F5Y
  • Community annotation for 1F5Y at PDBWiki (http://pdbwiki.org)
  • NMR Ensemble (OLDERADO: core, domain and representative structure database)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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