1D2J Signaling Protein date Sep 23, 1999
title Ldl Receptor Ligand-Binding Module 6
authors C.L.North, S.C.Blacklow
compound source
Molecule: Low-Density Lipoprotein Receptor
Chain: A
Fragment: Ligand-Binding Domain, Sixth Repeat
Synonym: Lr6
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmm-Lr6
methodSolution NMR
ligand CA enzyme
related structures by homologous chain: 1F8Z
Primary referenceSolution structure of the sixth LDL-A module of the LDL receptor., North CL, Blacklow SC, Biochemistry 2000 Mar 14;39(10):2564-71. PMID:10704205
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (198 Kb) [Save to disk]
  • LPC: Ligand-Protein Contacts for 1D2J
  • CSU: Contacts of Structural Units for 1D2J
  • Original NMR restraints for 1D2J from PDB
  • Retrieve 1D2J in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1D2J from S2C, [Save to disk]
  • View 1D2J 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 1D2J
  • 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 1D2J, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1d2ja_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1d2j from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [1d2j_A] [1d2j]
  • SWISS-PROT database: [P01130]
  • Domain organization of [LDLR_HUMAN] by SWISSPFAM
  • Domain found in 1D2J: [LDLa ] by SMART
  • Other resources with information on 1D2J
  • Community annotation for 1D2J 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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