3FII Hydrolase, Toxin Protein Transport date Dec 11, 2008
title Crystal Structure Of Clostridium Botulinum Neurotoxin Serotype F Catalytic Domain With An Inhibitor (Inh2)
authors R.Agarwal, S.Swaminathan
compound source
Molecule: Botulinum Neurotoxin Type F
Chain: A
Fragment: Residues 1-419, Catalytic Domain
Synonym: Bontf (Neurotoxin Type F)
Engineered: Yes
Organism_scientific: Clostridium Botulinum
Organism_taxid: 1491
Gene: Bontf
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Ripl
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b

Molecule: Fragment Of Vesicle-Associated Membrane Protein 2;
Chain: B
Fragment: Residues 27-58
Synonym: Vamp-2, Synaptobrevin-2
Engineered: Yes
Mutation: Yes

Synthetic: Yes
Other_details: Sequence Occurs In Homo Sapiens
symmetry Space Group: P 21 21 21
R_factor 0.246 R_Free 0.290
length a length b length c angle alpha angle beta angle gamma
55.592 70.353 113.929 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.17 Å
ligand 00C, NH2, ZN enzyme Hydrolase E.C. BRENDA


Primary referenceMode of VAMP substrate recognition and inhibition of Clostridium botulinum neurotoxin F., Agarwal R, Schmidt JJ, Stafford RG, Swaminathan S, Nat Struct Mol Biol. 2009 Jul;16(7):789-94. Epub 2009 Jun 21. PMID:19543288
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (78 Kb) [Save to disk]
  • Biological Unit Coordinates (3fii.pdb1.gz) 73 Kb
  • LPC: Ligand-Protein Contacts for 3FII
  • CSU: Contacts of Structural Units for 3FII
  • Likely Quarternary Molecular Structure file(s) for 3FII
  • Structure Factors (161 Kb)
  • Retrieve 3FII in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3FII from S2C, [Save to disk]
  • Re-refined 3fii structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3FII 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 3FII
  • 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 3FII, from MSDmotif at EBI
  • Fold representative 3fii from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3fii_B] [3fii] [3fii_A]
  • SWISS-PROT database: [P30996] [P63027]
  • Belongs to the synaptosomal vesicle fusion pore (svf-pore) family according to TCDB.
  • Domain organization of [BXF_CLOBO] [VAMP2_HUMAN] by SWISSPFAM
  • Other resources with information on 3FII
  • Community annotation for 3FII 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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