5EKV Translation date Nov 04, 2015
title Co-Crystal Structure Of Eif4e With Nucleotide Mimetic Inhibi
authors M.W.Nowicki, M.D.Walkinshaw, P.M.Fischer
compound source
Molecule: Eukaryotic Translation Initiation Factor 4e
Chain: A, C
Synonym: Eif4e,Eif-4f 25 Kda Subunit,Mrna Cap-Binding Prote
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Eif4e, Eif4el1, Eif4f
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Rosetta Plyss
Expression_system_plasmid: Pet11d

Molecule: Eukaryotic Translation Initiation Factor 4e-Bindi 1;
Chain: B, D
Fragment: Eif4e Binding Sequence, Unp Residues 51-64
Synonym: Eif4e-Binding Protein 1,Phosphorylated Heat- And A Protein Regulated By Insulin 1,Phas-I;
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Natural Sequence From 4ebp
symmetry Space Group: P 21 21 21
R_factor 0.267 R_Free 0.342
crystal
cell
length a length b length c angle alpha angle beta angle gamma
38.480 100.780 136.460 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.61 Å
ligand 5PQ enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, C


Primary referenceDesign of nucleotide-mimetic and non-nucleotide inhibitors of the translation initiation factor eIF4E: Synthesis, structural and functional characterisation., Soukarieh F, Nowicki MW, Bastide A, Poyry T, Jones C, Dudek K, Patwardhan G, Meullenet F, Oldham NJ, Walkinshaw MD, Willis AE, Fischer PM, Eur J Med Chem. 2016 Aug 24;124:200-217. doi: 10.1016/j.ejmech.2016.08.047. PMID:27592390
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (69 Kb) [Save to disk]
  • Biological Unit Coordinates (5ekv.pdb1.gz) 33 Kb
  • Biological Unit Coordinates (5ekv.pdb2.gz) 33 Kb
  • LPC: Ligand-Protein Contacts for 5EKV
  • CSU: Contacts of Structural Units for 5EKV
  • Structure Factors (80 Kb)
  • Retrieve 5EKV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5EKV from S2C, [Save to disk]
  • Re-refined 5ekv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5EKV 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 5EKV
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ekv] [5ekv_A] [5ekv_D] [5ekv_C] [5ekv_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5EKV
  • Community annotation for 5EKV at PDBWiki (http://pdbwiki.org)

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