2I4I Hydrolase date Aug 22, 2006
title Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
authors M.Hogbom, T.Karlberg, C.Arrowsmith, H.Berglund, R.D.Busam, R.Coll A.Edwards, M.Ehn, S.Flodin, A.Flores, S.Graslund, B.M.Hallberg, M.Hammarstrom, I.Johansson, T.Kotenyova, A.Magnusdottir, P.Nils P.Nordlund, T.Nyman, D.Ogg, C.Persson, J.Sagemark, P.Stenmark, M.Sundstrom, A.G.Thorsell, J.Uppenberg, S.Van Den Berg, K.Walld J.Weigelt, M.Welin, L.Holmberg-Schiavone, Structural Genomics Consortium (Sgc)
compound source
Molecule: Atp-Dependent Rna Helicase Ddx3x
Chain: A
Synonym: Dead Box Protein 3, X- Chromosomal, Helicase-Like Hlp2, Dead Box, X Isoform;
Ec: 3.6.1.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ddx3x
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic-Bsa4
symmetry Space Group: P 31 2 1
R_factor 0.187 R_Free 0.218
length a length b length c angle alpha angle beta angle gamma
67.288 67.288 253.470 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.20 Å
ligand AMP enzyme Hydrolase E.C.3.6.1 BRENDA

Primary referenceCrystal Structure of Conserved Domains 1 and 2 of the Human DEAD-box Helicase DDX3X in Complex with the Mononucleotide AMP., Hogbom M, Collins R, van den Berg S, Jenvert RM, Karlberg T, Kotenyova T, Flores A, Hedestam GB, Schiavone LH, J Mol Biol. 2007 Sep 7;372(1):150-9. Epub 2007 Jun 26. PMID:17631897
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (77 Kb) [Save to disk]
  • Biological Unit Coordinates (2i4i.pdb1.gz) 71 Kb
  • LPC: Ligand-Protein Contacts for 2I4I
  • CSU: Contacts of Structural Units for 2I4I
  • Likely Quarternary Molecular Structure file(s) for 2I4I
  • Structure Factors (248 Kb)
  • Retrieve 2I4I in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2I4I from S2C, [Save to disk]
  • Re-refined 2i4i structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2I4I 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 2I4I
  • 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 2I4I, from MSDmotif at EBI
  • Fold representative 2i4i from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2i4i_A] [2i4i]
  • SWISS-PROT database: [O00571]
  • Belongs to the eukaryotic nuclear pore complex (e-npc) family according to TCDB.
  • Domain organization of [DDX3X_HUMAN] by SWISSPFAM
  • Domains found in 2I4I: [DEXDc] [HELICc ] by SMART
  • Other resources with information on 2I4I
  • Community annotation for 2I4I at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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