5WYF Isomerase date Jan 12, 2017
title Structure Of Amino Acid Racemase, 2.12 A
authors H.Sakuraba, Y.Mutaguchi, J.Hayashi, T.Ohshima
compound source
Molecule: Isoleucine 2-Epimerase
Chain: A, B, C, D
Synonym: Bcaa Racemase
Engineered: Yes
Organism_scientific: Lactobacillus Buchneri
Organism_taxid: 1581
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcold Pros2
symmetry Space Group: P 1 21 1
R_factor 0.176 R_Free 0.221
length a length b length c angle alpha angle beta angle gamma
59.514 85.277 186.566 90.00 96.93 90.00
method X-Ray Diffractionresolution 2.12 Å
ligand CD, ILP enzyme Isomerase E.C. BRENDA
A, D, C, B

Primary referenceCrystal structure of the novel amino-acid racemase isoleucine 2-epimerase from Lactobacillus buchneri., Hayashi J, Mutaguchi Y, Minemura Y, Nakagawa N, Yoneda K, Ohmori T, Ohshima T, Sakuraba H, Acta Crystallogr D Struct Biol. 2017 May 1;73(Pt 5):428-437. doi:, 10.1107/S2059798317005332. Epub 2017 Apr 19. PMID:28471367
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (296 Kb) [Save to disk]
  • Biological Unit Coordinates (5wyf.pdb1.gz) 289 Kb
  • LPC: Ligand-Protein Contacts for 5WYF
  • CSU: Contacts of Structural Units for 5WYF
  • Structure Factors (1423 Kb)
  • Retrieve 5WYF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5WYF from S2C, [Save to disk]
  • Re-refined 5wyf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5WYF 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 5WYF
  • 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 5wyf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5wyf_B] [5wyf] [5wyf_A] [5wyf_D] [5wyf_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5WYF
  • Community annotation for 5WYF at PDBWiki (http://pdbwiki.org)

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