4Q4B Cell Adhesion date Apr 14, 2014
title Crystal Structure Of Limp-2 (Space Group C2221)
authors Y.Zhao, J.Ren, S.Padilla-Parra, L.E.Fry, D.I.Stuart
compound source
Molecule: Lysosome Membrane Protein 2
Chain: A
Fragment: Human Limp-2 Luminal Domain
Synonym: 85 Kda Lysosomal Membrane Sialoglycoprotein, Lgp85 Antigen-Like 2, Lysosome Membrane Protein II, Limp II, Scav Receptor Class B Member 2;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cd36l2, Limp2, Limpii, Scarb2
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell_line: Hek 293s Gnti-
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pneosec
symmetry Space Group: C 2 2 21
R_factor 0.221 R_Free 0.276
crystal
cell
length a length b length c angle alpha angle beta angle gamma
63.729 95.943 217.816 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.82 Å
ligand BMA, MAN, NA, NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceLysosome sorting of beta-glucocerebrosidase by LIMP-2 is targeted by the mannose 6-phosphate receptor., Zhao Y, Ren J, Padilla-Parra S, Fry EE, Stuart DI, Nat Commun. 2014 Jul 14;5:4321. doi: 10.1038/ncomms5321. PMID:25027712
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (156 Kb) [Save to disk]
  • Biological Unit Coordinates (4q4b.pdb1.gz) 149 Kb
  • LPC: Ligand-Protein Contacts for 4Q4B
  • CSU: Contacts of Structural Units for 4Q4B
  • Structure Factors (174 Kb)
  • Retrieve 4Q4B in mmCIF format [Save to disk]
  • Re-refined 4q4b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4Q4B 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 4Q4B
  • 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 4Q4B, from MSDmotif at EBI
  • Fold representative 4q4b from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4q4b_A] [4q4b]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4Q4B
  • Community annotation for 4Q4B at PDBWiki (http://pdbwiki.org)

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