5H4Y Metal Binding Protein date Nov 02, 2016
title Crystal Structure Of Human Synaptotagmin 5 C2a Domain
authors X.Qiu, Y.Gao, M.Teng, L.Niu
compound source
Molecule: Synaptotagmin-5
Chain: A
Fragment: Unp Residues 102-242
Synonym: Synaptotagmin V,Sytv
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Syt5
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: K12
Expression_system_plasmid: P28
symmetry Space Group: P 65
R_factor 0.171 R_Free 0.212
length a length b length c angle alpha angle beta angle gamma
93.966 93.966 28.052 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.90 Å
ligand ACT, CA enzyme

Primary referenceStructural analysis of Ca2+-binding pocket of synaptotagmin 5 C2A domain., Qiu X, Ge J, Gao Y, Teng M, Niu L, Int J Biol Macromol. 2016 Oct 25. pii: S0141-8130(16)32153-5. doi:, 10.1016/j.ijbiomac.2016.10.083. PMID:27793683
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (29 Kb) [Save to disk]
  • Biological Unit Coordinates (5h4y.pdb1.gz) 24 Kb
  • LPC: Ligand-Protein Contacts for 5H4Y
  • CSU: Contacts of Structural Units for 5H4Y
  • Structure Factors (135 Kb)
  • Retrieve 5H4Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5H4Y from S2C, [Save to disk]
  • Re-refined 5h4y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5H4Y 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 5H4Y
  • 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
  • Fold representative 5h4y from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5h4y_A] [5h4y]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5H4Y: [C2 ] by SMART
  • Other resources with information on 5H4Y
  • Community annotation for 5H4Y at PDBWiki (http://pdbwiki.org)

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