3G3B Hydrolase Immune System date Feb 02, 2009
title Structure Of A Lamprey Variable Lymphocyte Receptor Mutant In Complex With A Protein Antigen
authors L.Deng, C.A.Velikovsky, R.A.Mariuzza
compound source
Molecule: Variable Lymphocyte Receptor Vlrb.2d
Chain: A, C, E, G
Fragment: Variable Lymphocyte Receptor 2d13
Engineered: Yes
Mutation: Yes
Organism_scientific: Petromyzon Marinus
Organism_common: Sea Lamprey
Organism_taxid: 7757
Gene: Vlr
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Codonplus(De3)-Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pt7.7

Molecule: Lysozyme C
Chain: B, D, F, H
Synonym: 1,4-Beta-N-Acetylmuramidase C, Allergen Gal D Iv
Engineered: Yes

Organism_scientific: Gallus Gallus
Organism_common: Bantam,Chickens
Organism_taxid: 9031
Strain: Chicken
Gene: Lysozyme, Lyz
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.242 R_Free 0.286
length a length b length c angle alpha angle beta angle gamma
62.874 106.244 218.544 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
enzyme Hydrolase E.C. BRENDA
note 3G3B is a representative structure
H, F, D, B

Primary referenceStructure of a lamprey variable lymphocyte receptor in complex with a protein antigen., Velikovsky CA, Deng L, Tasumi S, Iyer LM, Kerzic MC, Aravind L, Pancer Z, Mariuzza RA, Nat Struct Mol Biol. 2009 Jul;16(7):725-30. Epub 2009 Jun 21. PMID:19543291
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (176 Kb) [Save to disk]
  • Biological Unit Coordinates (3g3b.pdb1.gz) 49 Kb
  • Biological Unit Coordinates (3g3b.pdb2.gz) 49 Kb
  • Biological Unit Coordinates (3g3b.pdb3.gz) 47 Kb
  • Biological Unit Coordinates (3g3b.pdb4.gz) 34 Kb
  • CSU: Contacts of Structural Units for 3G3B
  • Likely Quarternary Molecular Structure file(s) for 3G3B
  • Structure Factors (519 Kb)
  • Retrieve 3G3B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3G3B from S2C, [Save to disk]
  • Re-refined 3g3b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3G3B 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 3G3B
  • 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 3G3B, from MSDmotif at EBI
  • Fold representative 3g3b from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3g3b_H] [3g3b_F] [3g3b_D] [3g3b_A] [3g3b_G] [3g3b_C] [3g3b] [3g3b_E] [3g3b_B]
  • SWISS-PROT database: [D0VX19] [P00698]
  • Domain organization of [D0VX19_PETMA] [LYSC_CHICK] by SWISSPFAM
  • Domains found in 3G3B: [LRR] [LRRNT] [LRR_TYP] [LYZ1 ] by SMART
  • Other resources with information on 3G3B
  • Community annotation for 3G3B 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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