6NYC Metal Binding Protein date Feb 11, 2019
title Munc13-1 C2b-Domain, Calcium Free
authors D.R.Tomchick, J.Rizo, M.Machius, J.Lu
compound source
Molecule: Munc13-1
Chain: A
Fragment: C2b Domain, Residues 675-820
Synonym: Protein Unc-13 Homolog A
Engineered: Yes
Mutation: Yes
Organism_scientific: Rattus Norvegicus
Organism_common: Rat
Organism_taxid: 10116
Gene: Unc13a, Unc13h1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-Kt
symmetry Space Group: C 2 2 21
R_factor 0.209 R_Free 0.248
crystal
cell
length a length b length c angle alpha angle beta angle gamma
42.572 101.141 68.038 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.89 Å
ligand B3P, CL enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceMunc13 C2B domain is an activity-dependent Ca2+ regulator of synaptic exocytosis., Shin OH, Lu J, Rhee JS, Tomchick DR, Pang ZP, Wojcik SM, Camacho-Perez M, Brose N, Machius M, Rizo J, Rosenmund C, Sudhof TC, Nat Struct Mol Biol. 2010 Mar;17(3):280-8. Epub 2010 Feb 14. PMID:20154707
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (65 Kb) [Save to disk]
  • Biological Unit Coordinates (6nyc.pdb1.gz) 60 Kb
  • LPC: Ligand-Protein Contacts for 6NYC
  • CSU: Contacts of Structural Units for 6NYC
  • Structure Factors (345 Kb)
  • Retrieve 6NYC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6NYC from S2C, [Save to disk]
  • View 6NYC 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 6NYC
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6nyc_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6NYC
  • Community annotation for 6NYC at PDBWiki (http://pdbwiki.org)

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