3FIE Hydrolase, Toxin Protein Transport date Dec 11, 2008
title Crystal Structure Of Clostridium Botulinum Neurotoxin Serotype F Catalytic Domain With An Inhibitor (Inh1)
authors R.Agarwal, S.Swaminathan
compound source
Molecule: Botulinum Neurotoxin Type F
Chain: A, B
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: C, D
Fragment: Residues 22-58
Synonym: Vamp-2, Synaptobrevin-2
Engineered: Yes
Mutation: Yes

Synthetic: Yes
Other_details: Sequence Occurs In Homo Sapiens
symmetry Space Group: P 1
R_factor 0.228 R_Free 0.279
length a length b length c angle alpha angle beta angle gamma
55.637 61.389 70.027 94.24 89.92 113.27
method X-Ray Diffractionresolution 2.10 Å
ligand DCY, NH2, ZN enzyme Hydrolase E.C. BRENDA
A, B

D, C

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] (153 Kb) [Save to disk]
  • Biological Unit Coordinates (3fie.pdb1.gz) 76 Kb
  • Biological Unit Coordinates (3fie.pdb2.gz) 75 Kb
  • LPC: Ligand-Protein Contacts for 3FIE
  • CSU: Contacts of Structural Units for 3FIE
  • Likely Quarternary Molecular Structure file(s) for 3FIE
  • Structure Factors (363 Kb)
  • Retrieve 3FIE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3FIE from S2C, [Save to disk]
  • Re-refined 3fie structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3FIE 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 3FIE
  • 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 3FIE, from MSDmotif at EBI
  • Fold representative 3fie from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3fie] [3fie_D] [3fie_C] [3fie_A] [3fie_B]
  • 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 3FIE
  • Community annotation for 3FIE 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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