1N7D Lipid Transport date Nov 13, 2002
title Extracellular Domain Of The Ldl Receptor
authors G.Rudenko, L.Henry, K.Henderson, K.Ichtchenko, M.S.Brown, J.L.Gol J.Deisenhofer
compound source
Molecule: Low-Density Lipoprotein Receptor
Chain: A
Fragment: Extracellular Domain, Residues 1-699
Synonym: Ldl Receptor
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ldlr
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_vector_type: Baculovirus
symmetry Space Group: P 31 2 1
R_factor 0.381 R_Free 0.382
crystal
cell
length a length b length c angle alpha angle beta angle gamma
185.290 185.290 85.186 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.70 Å
ligand BMA, CA, KEG, MAN, NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructure of the LDL receptor extracellular domain at endosomal pH., Rudenko G, Henry L, Henderson K, Ichtchenko K, Brown MS, Goldstein JL, Deisenhofer J, Science 2002 Dec 20;298(5602):2353-8. Epub 2002 Nov 29. PMID:12459547
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (96 Kb) [Save to disk]
  • Biological Unit Coordinates (1n7d.pdb1.gz) 85 Kb
  • LPC: Ligand-Protein Contacts for 1N7D
  • CSU: Contacts of Structural Units for 1N7D
  • Likely Quarternary Molecular Structure file(s) for 1N7D
  • Retrieve 1N7D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1N7D from S2C, [Save to disk]
  • View 1N7D 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 1N7D
  • 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 1N7D, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1n7da7, region A:125-174 [Jmol] [rasmolscript] [script source]
        - Domain d1n7da8, region A:175-211 [Jmol] [rasmolscript] [script source]
        - Domain d1n7da9, region A:212-251 [Jmol] [rasmolscript] [script source]
        - Domain d1n7daa, region A:252-295 [Jmol] [rasmolscript] [script source]
        - Domain d1n7da2, region A:296-332 [Jmol] [rasmolscript] [script source]
        - Domain d1n7da3, region A:333-376 [Jmol] [rasmolscript] [script source]
        - Domain d1n7da1, region A:377-642 [Jmol] [rasmolscript] [script source]
        - Domain d1n7da5, region A:44-83 [Jmol] [rasmolscript] [script source]
        - Domain d1n7da4, region A:643-693 [Jmol] [rasmolscript] [script source]
        - Domain d1n7da6, region A:84-124 [Jmol] [rasmolscript] [script source]
  • Fold representative 1n7d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1n7d] [1n7d_A]
  • SWISS-PROT database: [P01130]
  • Domain organization of [LDLR_HUMAN] by SWISSPFAM
  • Domains found in 1N7D: [EGF_CA] [EGF_like] [LDLa] [LY ] by SMART
  • Other resources with information on 1N7D
  • Community annotation for 1N7D 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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