5H1Y Hydrolase date Oct 13, 2016
title Crystal Structure Of The Ddx41 Dead Domain In Complex With S Mg2+
authors Y.Jiang, S.Ouyang, Z.J.Liu
compound source
Molecule: Probable Atp-Dependent Rna Helicase Ddx41
Chain: A, B
Fragment: Unp Residues 153-410
Synonym: Dead Box Protein 41,Dead Box Protein Abstrakt Homo
Ec: 3.6.4.13
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ddx41, Abs
Expression_system: Escherichia Coli-Pichia Pastoris Shuttle Ppparg4;
Expression_system_taxid: 1182032
Expression_system_vector: Ppparg4
symmetry Space Group: P 1 21 1
R_factor 0.186 R_Free 0.233
crystal
cell
length a length b length c angle alpha angle beta angle gamma
43.881 62.746 92.881 90.00 94.32 90.00
method X-Ray Diffractionresolution 2.26 Å
ligand MG, SO4 enzyme Hydrolase E.C.3.6.4.13 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural and functional analyses of human DDX41 DEAD domain., Jiang Y, Zhu Y, Qiu W, Liu YJ, Cheng G, Liu ZJ, Ouyang S, Protein Cell. 2017 Jan;8(1):72-76. doi: 10.1007/s13238-016-0351-9. PMID:27928732
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (85 Kb) [Save to disk]
  • Biological Unit Coordinates (5h1y.pdb1.gz) 41 Kb
  • Biological Unit Coordinates (5h1y.pdb2.gz) 41 Kb
  • LPC: Ligand-Protein Contacts for 5H1Y
  • CSU: Contacts of Structural Units for 5H1Y
  • Structure Factors (480 Kb)
  • Retrieve 5H1Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5H1Y from S2C, [Save to disk]
  • Re-refined 5h1y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5H1Y 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 5H1Y
  • 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: [5h1y] [5h1y_B] [5h1y_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5H1Y
  • Community annotation for 5H1Y at PDBWiki (http://pdbwiki.org)

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