5YAK Oxidoreductase date Sep 01, 2017
title The Crystal Structure Of Human Iyd Thr239 Mutant With Ligand Fluorotyrosine (F-Tyr)
authors J.M.Hu, S.E.Rokita, J.Schlessman
compound source
Molecule: Iodotyrosine Deiodinase 1
Chain: A, B, C, D, E, F
Fragment: Unp Residues 32-289
Synonym: Iyd-1,Iodotyrosine Dehalogenase 1
Engineered: Yes
Mutation: Yes
Other_details: Fmn(Flavin Mononucleotide) Yof(3-Monofluorot
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Iyd, C6orf71, Dehal1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta 2(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28-Sumo
symmetry Space Group: P 61
R_factor 0.183 R_Free 0.226
length a length b length c angle alpha angle beta angle gamma
105.079 105.079 300.202 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.30 Å
enzyme Oxidoreductase E.C. BRENDA
F, A, D, C, E, B
  • iodide peroxidase activity

  • Primary referenceRedox control of iodotyrosine deiodinase., Hu J, Su Q, Schlessman J, Rokita SE, Protein Sci. 2018 Jul 27. doi: 10.1002/pro.3479. PMID:30052294
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (234 Kb) [Save to disk]
  • Biological Unit Coordinates (5yak.pdb1.gz) 78 Kb
  • Biological Unit Coordinates (5yak.pdb2.gz) 78 Kb
  • Biological Unit Coordinates (5yak.pdb3.gz) 78 Kb
  • CSU: Contacts of Structural Units for 5YAK
  • Structure Factors (2435 Kb)
  • Retrieve 5YAK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5YAK from S2C, [Save to disk]
  • View 5YAK 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 5YAK
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5yak from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5yak_A] [5yak_C] [5yak_F] [5yak_D] [5yak_B] [5yak_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5YAK
  • Community annotation for 5YAK at PDBWiki (http://pdbwiki.org)

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