5MOY Hydrolase date Dec 14, 2016
title Crystal Structure Of The Bonta2 Receptor-Binding Domain In With The Luminal Domain Of Its Neuronal Receptor Sv2c
authors R.M.Benoit, M.A.Scharer
compound source
Molecule: Botulinum Neurotoxin Type A
Chain: A
Fragment: Unp Residues 871-1296
Synonym: Bonta,Bontoxilysin-A,Botox
Ec: 3.4.24.69
Engineered: Yes
Organism_scientific: Clostridium Botulinum
Organism_taxid: 1491
Gene: Bota, Atx, Bna
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Synaptic Vesicle Glycoprotein 2c
Chain: B
Fragment: Unp Residues 456-574
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sv2c, Kiaa1054
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.195 R_Free 0.251
crystal
cell
length a length b length c angle alpha angle beta angle gamma
47.740 91.570 147.660 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand 2PE, EDO enzyme Hydrolase E.C.3.4.24.69 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of the BoNT/A2 receptor-binding domain in complex with the luminal domain of its neuronal receptor SV2C., Benoit RM, Scharer MA, Wieser MM, Li X, Frey D, Kammerer RA, Sci Rep. 2017 Mar 2;7:43588. doi: 10.1038/srep43588. PMID:28252640
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (171 Kb) [Save to disk]
  • Biological Unit Coordinates (5moy.pdb1.gz) 165 Kb
  • LPC: Ligand-Protein Contacts for 5MOY
  • CSU: Contacts of Structural Units for 5MOY
  • Structure Factors (240 Kb)
  • Retrieve 5MOY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5MOY from S2C, [Save to disk]
  • Re-refined 5moy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5MOY 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 5MOY
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5moy_B] [5moy_A] [5moy]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5MOY
  • Community annotation for 5MOY at PDBWiki (http://pdbwiki.org)

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