5EK0 Metal Transport date Nov 03, 2015
title Human Nav1.7-Vsd4-Navab In Complex With Gx-936.
authors S.Ahuja, S.Mukund, M.A.Starovasnik, C.M.Koth, J.Payandeh
compound source
Molecule: Chimera Of Bacterial Ion Transport Protein And Hu Channel Protein Type 9 Subunit Alpha;
Chain: A, B, C, D
Synonym: Euroendocrine Sodium Channel,Hne-Na,Peripheral Sod Channel 1,Pn1,Sodium Channel Protein Type Ix Subunit Alpha, Gated Sodium Channel Subunit Alpha Nav1.7;
Engineered: Yes
Organism_scientific: Arcobacter Butzleri, Homo Sapiens
Organism_taxid: 367737, 9606
Strain: Rm4018
Gene: Abu_1752, Scn9a, Nena
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111
symmetry Space Group: C 2 2 21
R_factor 0.243 R_Free 0.272
length a length b length c angle alpha angle beta angle gamma
169.420 188.830 171.130 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.53 Å
ligand 5P2, PX4 enzyme
subcellular loc. Membrane localization by OPM: Bacterial Gram-negative inner membrane
Gene ABU
A, D, C, B

Primary referenceStructural basis of Nav1.7 inhibition by an isoform-selective small-molecule antagonist., Ahuja S, Mukund S, Deng L, Khakh K, Chang E, Ho H, Shriver S, Young C, Lin S, Johnson JP Jr, Wu P, Li J, Coons M, Tam C, Brillantes B, Sampang H, Mortara K, Bowman KK, Clark KR, Estevez A, Xie Z, Verschoof H, Grimwood M, Dehnhardt C, Andrez JC, Focken T, Sutherlin DP, Safina BS, Starovasnik MA, Ortwine DF, Franke Y, Cohen CJ, Hackos DH, Koth CM, Payandeh J, Science. 2015 Dec 18;350(6267):aac5464. doi: 10.1126/science.aac5464. PMID:26680203
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (185 Kb) [Save to disk]
  • Biological Unit Coordinates (5ek0.pdb1.gz) 175 Kb
  • LPC: Ligand-Protein Contacts for 5EK0
  • CSU: Contacts of Structural Units for 5EK0
  • Structure Factors (928 Kb)
  • Retrieve 5EK0 in mmCIF format [Save to disk]
  • Re-refined 5ek0 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5EK0 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 5EK0
  • 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 5ek0 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ek0_B] [5ek0] [5ek0_D] [5ek0_A] [5ek0_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5EK0
  • Community annotation for 5EK0 at PDBWiki (http://pdbwiki.org)

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