1J8E Signaling Protein date May 21, 2001
title Crystal Structure Of Ligand-Binding Repeat Cr7 From Lrp
authors M.Simonovic, K.Dolmer, W.Huang, D.K.Strickland, K.Volz, P.G.W.Gettins
compound source
Molecule: Low-Density Lipoprotein Receptor-Related Protein 1;
Chain: A
Fragment: Complement-Like Repeat 7 (Cr7), Ldl-Receptor Class A 7;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-2t
symmetry Space Group: P 21 21 21
R_factor 0.186 R_Free 0.222
crystal
cell
length a length b length c angle alpha angle beta angle gamma
27.588 35.359 36.288 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.85 Å
ligand CA enzyme
Primary referenceCalcium coordination and pH dependence of the calcium affinity of ligand-binding repeat CR7 from the LRP. Comparison with related domains from the LRP and the LDL receptor., Simonovic M, Dolmer K, Huang W, Strickland DK, Volz K, Gettins PG, Biochemistry 2001 Dec 18;40(50):15127-34. PMID:11735395
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (12 Kb) [Save to disk]
  • Biological Unit Coordinates (1j8e.pdb1.gz) 8 Kb
  • LPC: Ligand-Protein Contacts for 1J8E
  • CSU: Contacts of Structural Units for 1J8E
  • Likely Quarternary Molecular Structure file(s) for 1J8E
  • Structure Factors (35 Kb)
  • Retrieve 1J8E in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1J8E from S2C, [Save to disk]
  • Re-refined 1j8e structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1J8E 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 1J8E
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1J8E, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1j8ea_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1j8e 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: [1j8e_A] [1j8e]
  • SWISS-PROT database: [Q07954]
  • Domain organization of [LRP1_HUMAN] by SWISSPFAM
  • Domain found in 1J8E: [LDLa ] by SMART
  • Other resources with information on 1J8E
  • Community annotation for 1J8E 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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