1YXJ Lipid Binding Protein date Feb 22, 2005
title Crystal Structure Of Human Lectin-Like Oxidized Low-Density Lipoprotein Receptor 1 (Lox-1) At Low Ph
authors I.Ohki, T.Ishigaki, T.Oyama, S.Matsunaga, Q.Xie, M.Ohnishi- Kameyama, T.Murata, D.Tsuchiya, S.Machida, K.Morikawa, S.Tate
compound source
Molecule: Oxidised Low Density Lipoprotein (Lectin-Like) Receptor 1;
Chain: A, B
Fragment: Ligand-Binding Domain
Synonym: Lox-1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a
symmetry Space Group: P 21 21 21
R_factor 0.211 R_Free 0.234
length a length b length c angle alpha angle beta angle gamma
62.636 68.828 79.133 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.78 Å
ligand EDO, MSE enzyme
related structures by homologous chain: 1YPQ, 1YPU
Primary referenceCrystal structure of human lectin-like, oxidized low-density lipoprotein receptor 1 ligand binding domain and its ligand recognition mode to OxLDL., Ohki I, Ishigaki T, Oyama T, Matsunaga S, Xie Q, Ohnishi-Kameyama M, Murata T, Tsuchiya D, Machida S, Morikawa K, Tate S, Structure. 2005 Jun;13(6):905-17. PMID:15939022
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (51 Kb) [Save to disk]
  • Biological Unit Coordinates (1yxj.pdb1.gz) 47 Kb
  • LPC: Ligand-Protein Contacts for 1YXJ
  • CSU: Contacts of Structural Units for 1YXJ
  • Likely Quarternary Molecular Structure file(s) for 1YXJ
  • Structure Factors (294 Kb)
  • Retrieve 1YXJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YXJ from S2C, [Save to disk]
  • Re-refined 1yxj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1YXJ 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 1YXJ
  • 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 1YXJ, from MSDmotif at EBI
  • Fold representative 1yxj from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yxj] [1yxj_B] [1yxj_A]
  • SWISS-PROT database: [P78380]
  • Domain organization of [OLR1_HUMAN] by SWISSPFAM
  • Domain found in 1YXJ: [CLECT ] by SMART
  • Other resources with information on 1YXJ
  • Community annotation for 1YXJ 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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