5FDY Membrane Protein date Dec 16, 2015
title Crystal Structure Of The Voltage-Gated Sodium Channel Beta 2 Extracellular Domain, C72ac75a Mutant
authors S.Das, F.Van Petegem
compound source
Molecule: Sodium Channel Subunit Beta-2
Chain: A, B
Fragment: Unp Residues 30-153
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Scn2b, Unq326pro386
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor 0.156 R_Free 0.185
length a length b length c angle alpha angle beta angle gamma
28.386 36.180 59.186 89.96 89.99 76.36
method X-Ray Diffractionresolution 1.85 Å
ligand GOL enzyme
A, B

Primary referenceBinary architecture of the Nav1.2-beta2 signaling complex., Das S, Gilchrist J, Bosmans F, Van Petegem F, Elife. 2016 Feb 19;5. pii: e10960. doi: 10.7554/eLife.10960. PMID:26894959
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (56 Kb) [Save to disk]
  • Biological Unit Coordinates (5fdy.pdb1.gz) 27 Kb
  • Biological Unit Coordinates (5fdy.pdb2.gz) 26 Kb
  • LPC: Ligand-Protein Contacts for 5FDY
  • CSU: Contacts of Structural Units for 5FDY
  • Structure Factors (328 Kb)
  • Retrieve 5FDY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5FDY from S2C, [Save to disk]
  • Re-refined 5fdy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5FDY 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 5FDY
  • 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 5fdy from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5fdy_B] [5fdy_A] [5fdy]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5FDY: [IG ] by SMART
  • Other resources with information on 5FDY
  • Community annotation for 5FDY at PDBWiki (http://pdbwiki.org)

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