2YC1 Immune System Toxin date Mar 10, 2011
title Crystal Structure Of The Human Derived Single Chain Antibody (Scfv) 9004g In Complex With Cn2 Toxin From The Scorpion Ce Noxius Hoffmann
authors J.C.Canul-Tec, L.Riano-Umbarila, E.Rudino-Pinera, B.Becerril, L.D.Possani, A.Torres-Larios
compound source
Molecule: Single Chain Antibody Fragment 9004g
Chain: A, D
Fragment: Heavy Chain
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 83333
Expression_system_strain: K-12
Expression_system_variant: Tg1
Expression_system_vector_type: Plasmid
Expression_system_vector: Psyn
Expression_system_plasmid: Psyn1

Molecule: Single Chain Antibody Fragment 9004g
Chain: B, E
Fragment: Light Chain
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 83333
Expression_system_strain: K-12
Expression_system_variant: Tg1
Expression_system_vector_type: Plasmid
Expression_system_vector: Psyn
Expression_system_plasmid: Psyn1

Molecule: Beta-Mammal Toxin Cn2
Chain: C, F
Synonym: Cn2 Toxin, Toxin 2, Toxin II.9.2.2

Organism_scientific: Centruroides Noxius Hoffmann
Organism_common: Mexican Scorpion
Organism_taxid: 6878
symmetry Space Group: F 2 3
R_factor 0.186 R_Free 0.212
crystal
cell
length a length b length c angle alpha angle beta angle gamma
219.709 219.709 219.709 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand GOL enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, C
  • toxin activity


  • Primary referenceStructural Basis of Neutralization of the Major Toxic Component from the Scorpion Centruroides noxius Hoffmann by a Human-derived Single-chain Antibody Fragment., Canul-Tec JC, Riano-Umbarila L, Rudino-Pinera E, Becerril B, Possani LD, Torres-Larios A, J Biol Chem. 2011 Jun 10;286(23):20892-900. Epub 2011 Apr 13. PMID:21489992
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (111 Kb) [Save to disk]
  • Biological Unit Coordinates (2yc1.pdb1.gz) 54 Kb
  • Biological Unit Coordinates (2yc1.pdb2.gz) 54 Kb
  • LPC: Ligand-Protein Contacts for 2YC1
  • CSU: Contacts of Structural Units for 2YC1
  • Structure Factors (1023 Kb)
  • Retrieve 2YC1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YC1 from S2C, [Save to disk]
  • Re-refined 2yc1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2YC1 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 2YC1
  • 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
  • 3D motif for 2YC1, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2yc1_F] [2yc1_D] [2yc1] [2yc1_C] [2yc1_E] [2yc1_B] [2yc1_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 2YC1: [IGv] [Knot1 ] by SMART
  • Other resources with information on 2YC1
  • Community annotation for 2YC1 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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