1YPQ Immune System date Jan 31, 2005
title Human Oxidized Low Density Lipoprotein Receptor Lox-1 Dioxane Complex
authors H.Park, F.G.Adsit, J.C.Boyington
compound source
Molecule: Oxidised Low Density Lipoprotein (Lectin-Like) Receptor 1;
Chain: A, B
Fragment: C-Type Lectin-Like Domain (Residues 136-273)
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Origami B (De3)
Expression_system_plasmid: Pet15b
symmetry Space Group: C 1 2 1
R_factor 0.177 R_Free 0.192
length a length b length c angle alpha angle beta angle gamma
70.700 49.100 76.300 90.00 98.50 90.00
method X-Ray Diffractionresolution 1.40 Å
ligand DIO enzyme
related structures by homologous chain: 1YXJ
Primary referenceThe 1.4 anstrom crystal structure of the human oxidized low density lipoprotein receptor lox-1., Park H, Adsit FG, Boyington JC, J Biol Chem 2005 Apr 8;280(14):13593-9. Epub 2005 Feb 5. PMID:15695803
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (55 Kb) [Save to disk]
  • Biological Unit Coordinates (1ypq.pdb1.gz) 51 Kb
  • LPC: Ligand-Protein Contacts for 1YPQ
  • CSU: Contacts of Structural Units for 1YPQ
  • Likely Quarternary Molecular Structure file(s) for 1YPQ
  • Structure Factors (724 Kb)
  • Retrieve 1YPQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YPQ from S2C, [Save to disk]
  • Re-refined 1ypq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1YPQ 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 1YPQ
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Conformational Epitope Prediction for 1YPQ 1YPQA 1YPQB from the CEP Server.
  • 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 1YPQ, from MSDmotif at EBI
  • Fold representative 1ypq from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1ypq_A] [1ypq] [1ypq_B]
  • SWISS-PROT database: [P78380]
  • Domain organization of [OLR1_HUMAN] by SWISSPFAM
  • Domain found in 1YPQ: [CLECT ] by SMART
  • Other resources with information on 1YPQ
  • Community annotation for 1YPQ 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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