4D4Z Oxidoreductase date Oct 31, 2014
title Structure Of Human Deoxyhypusine Hydroxylase In Complex With
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;
Ec: 1.14.99.29
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: Pgex-6p-1
symmetry Space Group: P 1 21 1
R_factor 0.17024 R_Free 0.19283
crystal
cell
length a length b length c angle alpha angle beta angle gamma
46.051 70.175 101.275 90.00 102.71 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand B3P, FE, GOL, OH enzyme Oxidoreductase E.C.1.14.99.29 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
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] (103 Kb) [Save to disk]
  • Biological Unit Coordinates (4d4z.pdb1.gz) 51 Kb
  • Biological Unit Coordinates (4d4z.pdb2.gz) 50 Kb
  • LPC: Ligand-Protein Contacts for 4D4Z
  • CSU: Contacts of Structural Units for 4D4Z
  • Structure Factors (1268 Kb)
  • Retrieve 4D4Z in mmCIF format [Save to disk]
  • Re-refined 4d4z structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4D4Z 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 4D4Z
  • 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 4D4Z, from MSDmotif at EBI
  • Fold representative 4d4z from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4d4z_B] [4d4z] [4d4z_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4D4Z: [EZ_HEAT ] by SMART
  • Other resources with information on 4D4Z
  • Community annotation for 4D4Z at PDBWiki (http://pdbwiki.org)

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