1YPO Immune System date Jan 31, 2005
title Human Oxidized Low Density Lipoprotein Receptor Lox-1 P3 1 21 Space Group
authors H.Park, F.G.Adsit, J.C.Boyington
compound source
Molecule: Oxidised Low Density Lipoprotein (Lectin-Like) Receptor 1;
Chain: A, B, C, D, E, F, G, H
Fragment: C-Type Lectin-Like Domain (Residues 142-273)
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: P 31 2 1
R_factor 0.228 R_Free 0.285
crystal
cell
length a length b length c angle alpha angle beta angle gamma
97.700 97.700 215.100 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.00 Å
related structures by homologous chain: 1YXK
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] (173 Kb) [Save to disk]
  • Biological Unit Coordinates (1ypo.pdb1.gz) 44 Kb
  • Biological Unit Coordinates (1ypo.pdb2.gz) 44 Kb
  • Biological Unit Coordinates (1ypo.pdb3.gz) 44 Kb
  • Biological Unit Coordinates (1ypo.pdb4.gz) 44 Kb
  • CSU: Contacts of Structural Units for 1YPO
  • Likely Quarternary Molecular Structure file(s) for 1YPO
  • Structure Factors (304 Kb)
  • Retrieve 1YPO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YPO from S2C, [Save to disk]
  • Re-refined 1ypo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1YPO 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 1YPO
  • 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 1YPO, from MSDmotif at EBI
  • Fold representative 1ypo from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1ypo_H] [1ypo_E] [1ypo_A] [1ypo_D] [1ypo_F] [1ypo_C] [1ypo] [1ypo_B] [1ypo_G]
  • SWISS-PROT database: [P78380]
  • Domain organization of [OLR1_HUMAN] by SWISSPFAM
  • Domain found in 1YPO: [CLECT ] by SMART
  • Other resources with information on 1YPO
  • Community annotation for 1YPO 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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