3VLG Lipid Binding Protein date Dec 01, 2011
title Crystal Structure Of The W150a Mutant Lox-1 Ctld Showing Imp Oxldl Binding
authors S.Nakano, M.Sugihara, R.Yamada, K.Katayanagi, S.Tate
compound source
Molecule: Oxidized Low-Density Lipoprotein Receptor 1
Chain: A
Fragment: C-Type Lectin-Like Domain
Synonym: Ox-Ldl Receptor 1, C-Type Lectin Domain Family 8 M Lectin-Like Oxidized Ldl Receptor 1;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Olr1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 41 21 2
R_factor 0.179 R_Free 0.246
length a length b length c angle alpha angle beta angle gamma
62.244 62.244 76.671 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
Primary referenceStructural implication for the impaired binding of W150A mutant LOX-1 to oxidized low density lipoprotein, OxLDL., Nakano S, Sugihara M, Yamada R, Katayanagi K, Tate SI, Biochim Biophys Acta. 2012 Feb 18;1824(5):739-749. PMID:22369967
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (27 Kb) [Save to disk]
  • Biological Unit Coordinates (3vlg.pdb1.gz) 22 Kb
  • CSU: Contacts of Structural Units for 3VLG
  • Structure Factors (103 Kb)
  • Retrieve 3VLG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VLG from S2C, [Save to disk]
  • Re-refined 3vlg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3VLG 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 3VLG
  • 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 3VLG, from MSDmotif at EBI
  • Fold representative 3vlg from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3vlg_A] [3vlg]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3VLG: [CLECT ] by SMART
  • Other resources with information on 3VLG
  • Community annotation for 3VLG at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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