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
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

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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