3E6J Immune System date Aug 15, 2008
title Crystal Structure Of Variable Lymphocyte Receptor (Vlr) Rbc3 Complex With H-Trisaccharide
authors B.W.Han, B.R.Herrin, M.D.Cooper, I.A.Wilson
compound source
Molecule: Variable Lymphocyte Receptor Diversity Region
Chain: A
Fragment: Ectodomain
Engineered: Yes
Organism_scientific: Petromyzon Marinus
Organism_common: Marine Lamprey
Organism_taxid: 7757
Gene: Vlr
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_strain: Hi5
Expression_system_vector_type: Baculoviral Expression
Expression_system_plasmid: Pbac6
symmetry Space Group: P 1 21 1
R_factor 0.146 R_Free 0.182
length a length b length c angle alpha angle beta angle gamma
54.221 48.564 55.477 90.00 116.51 90.00
method X-Ray Diffractionresolution 1.67 Å
ligand FUC, GAL, GOL, NAG, SO4 enzyme
Primary referenceAntigen recognition by variable lymphocyte receptors., Han BW, Herrin BR, Cooper MD, Wilson IA, Science. 2008 Sep 26;321(5897):1834-7. PMID:18818359
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (47 Kb) [Save to disk]
  • Biological Unit Coordinates (3e6j.pdb1.gz) 42 Kb
  • LPC: Ligand-Protein Contacts for 3E6J
  • CSU: Contacts of Structural Units for 3E6J
  • Likely Quarternary Molecular Structure file(s) for 3E6J
  • Structure Factors (424 Kb)
  • Retrieve 3E6J in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3E6J from S2C, [Save to disk]
  • Re-refined 3e6j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3E6J 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 3E6J
  • 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 3E6J, from MSDmotif at EBI
  • Fold representative 3e6j from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3e6j_A] [3e6j]
  • SWISS-PROT database: [Q2VGE8]
  • Domain organization of [Q2VGE8_PETMA] by SWISSPFAM
  • Domains found in 3E6J: [LRR] [LRRCT] [LRRNT] [LRR_TYP ] by SMART
  • Other resources with information on 3E6J
  • Community annotation for 3E6J 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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