3F00 Metal Binding Protein date Oct 24, 2008
title Crystal Structure Of Synaptotagmin I C2a Domain With Cu(II)
authors F.Guo, R.Dakshinamurthy, S.K.K.Thallapuranam, J.Sakon
compound source
Molecule: Synaptotagmin-1
Chain: A
Fragment: Unp Residues 141-266
Synonym: Synaptotagmin I, Syti, P65
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Syt1, Svp65, Syt
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
symmetry Space Group: P 1 21 1
R_factor 0.201 R_Free 0.244
crystal
cell
length a length b length c angle alpha angle beta angle gamma
41.647 38.363 44.016 90.00 98.37 90.00
method X-Ray Diffractionresolution 1.36 Å
ligand CU, MHO, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (60 Kb) [Save to disk]
  • Biological Unit Coordinates (3f00.pdb1.gz) 55 Kb
  • LPC: Ligand-Protein Contacts for 3F00
  • CSU: Contacts of Structural Units for 3F00
  • Structure Factors (348 Kb)
  • Retrieve 3F00 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3F00 from S2C, [Save to disk]
  • Re-refined 3f00 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3F00 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 3F00
  • 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 3F00, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3f00_A] [3f00]
  • SWISS-PROT database: [P21579]
  • Belongs to the synaptosomal vesicle fusion pore (svf-pore) family according to TCDB.
  • Domain organization of [SYT1_HUMAN] by SWISSPFAM
  • Domain found in 3F00: [C2 ] by SMART
  • Other resources with information on 3F00
  • Community annotation for 3F00 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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