4D50 Oxidoreductase date Oct 31, 2014
title Structure Of Human Deoxyhypusine Hydroxylase
authors Z.Han, N.Sakai, R.Hilgenfeld
compound source
Molecule: Deoxyhypusine Hydroxylase
Chain: A, B
Synonym: Hdohh, Deoxyhypusine Dioxygenase, Deoxyhypusine Monooxygenase, Heat-Like Repeat-Containing Protein 1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_vector: Pgex-6p-1
symmetry Space Group: P 1 21 1
R_factor 0.20261 R_Free 0.24650
length a length b length c angle alpha angle beta angle gamma
45.933 48.636 124.087 90.00 99.27 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand FE, GAI, PER enzyme Oxidoreductase E.C. BRENDA
A, B

Primary referenceCrystal Structure of the Peroxo-diiron(III) Intermediate of Deoxyhypusine Hydroxylase, an Oxygenase Involved in Hypusination., Han Z, Sakai N, Bottger LH, Klinke S, Hauber J, Trautwein AX, Hilgenfeld R, Structure. 2015 Apr 9. pii: S0969-2126(15)00080-5. doi:, 10.1016/j.str.2015.03.002. PMID:25865244
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (104 Kb) [Save to disk]
  • Biological Unit Coordinates (4d50.pdb1.gz) 51 Kb
  • Biological Unit Coordinates (4d50.pdb2.gz) 50 Kb
  • LPC: Ligand-Protein Contacts for 4D50
  • CSU: Contacts of Structural Units for 4D50
  • Structure Factors (1079 Kb)
  • Retrieve 4D50 in mmCIF format [Save to disk]
  • Re-refined 4d50 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4D50 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 4D50
  • 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
  • 3D motif for 4D50, from MSDmotif at EBI
  • Fold representative 4d50 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4d50] [4d50_A] [4d50_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4D50: [EZ_HEAT ] by SMART
  • Other resources with information on 4D50
  • Community annotation for 4D50 at PDBWiki (http://pdbwiki.org)

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