3M18 Immune System date Mar 04, 2010
title Crystal Structure Of Variable Lymphocyte Receptor Vlra.R2.1 With Hen Egg Lysozyme
authors L.Deng, C.A.Velikovsky, R.A.Mariuzza
compound source
Molecule: Variable Lymphocyte Receptor A Diversity Region
Chain: A
Fragment: Ectodomain
Engineered: Yes
Organism_scientific: Petromyzon Marinus
Organism_common: Marine Lamprey
Organism_taxid: 7757
Gene: Vlra
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Codonplus(De3)
Expression_system_vector_type: Plasmid
Expression_system_vector: Pt7-7

Molecule: Lysozyme C
Chain: B
Synonym: 1,4-Beta-N-Acetylmuramidase C, Allergen Gal D Iv
Ec: 3.2.1.17

Organism_scientific: Gallus Gallus
Organism_common: Bantam,Chickens
Organism_taxid: 9031
symmetry Space Group: P 1 21 1
R_factor 0.181 R_Free 0.240
crystal
cell
length a length b length c angle alpha angle beta angle gamma
46.794 68.116 59.751 90.00 110.94 90.00
method X-Ray Diffractionresolution 1.95 Å
ligand PO4 enzyme Hydrolase E.C.3.2.1.17 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
B


Primary referenceA structural basis for antigen recognition by the T cell-like lymphocytes of sea lamprey., Deng L, Velikovsky CA, Xu G, Iyer LM, Tasumi S, Kerzic MC, Flajnik MF, Aravind L, Pancer Z, Mariuzza RA, Proc Natl Acad Sci U S A. 2010 Jul 8. PMID:20616002
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (67 Kb) [Save to disk]
  • Biological Unit Coordinates (3m18.pdb1.gz) 63 Kb
  • LPC: Ligand-Protein Contacts for 3M18
  • CSU: Contacts of Structural Units for 3M18
  • Structure Factors (228 Kb)
  • Retrieve 3M18 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3M18 from S2C, [Save to disk]
  • Re-refined 3m18 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3M18 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 3M18
  • 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 3M18, from MSDmotif at EBI
  • Fold representative 3m18 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3m18_A] [3m18_B] [3m18]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3M18: [LRRNT] [LRR_TYP] [LYZ1 ] by SMART
  • Other resources with information on 3M18
  • Community annotation for 3M18 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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