3LY5 Hydrolase date Feb 26, 2010
title Ddx18 Dead-Domain
authors P.Schutz, T.Karlberg, C.H.Arrowsmith, H.Berglund, C.Bountra, R.Co A.M.Edwards, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, A.Jo I.Johansson, A.Kallas, P.Kraulis, T.Kotenyova, A.Kotzsch, N.Mark M.Moche, T.K.Nielsen, P.Nordlund, T.Nyman, C.Persson, A.K.Roos, M.I.Siponen, L.Svensson, A.G.Thorsell, L.Tresaugues, S.Van Den E.Wahlberg, J.Weigelt, M.Welin, M.Wisniewska, H.M.Schuler, Struc Genomics Consortium (Sgc)
compound source
Molecule: Atp-Dependent Rna Helicase Ddx18
Chain: A, B
Fragment: Dead-Domain, Residues 149-387
Synonym: Dead Box Protein 18, Myc-Regulated Dead Box Protei
Ec: 3.6.1.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ddx18
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Gold Prare2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic-Bsa4
symmetry Space Group: P 31
R_factor 0.246 R_Free 0.274
crystal
cell
length a length b length c angle alpha angle beta angle gamma
41.340 41.340 230.541 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.80 Å
ligand MG, PO4, SCN enzyme Hydrolase E.C.3.6.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceComparative structural analysis of human DEAD-box RNA helicases., Schutz P, Karlberg T, van den Berg S, Collins R, Lehtio L, Hogbom M, Holmberg-Schiavone L, Tempel W, Park HW, Hammarstrom M, Moche M, Thorsell AG, Schuler H, PLoS One. 2010 Sep 30;5(9). pii: e12791. PMID:20941364
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (67 Kb) [Save to disk]
  • Biological Unit Coordinates (3ly5.pdb1.gz) 32 Kb
  • Biological Unit Coordinates (3ly5.pdb2.gz) 32 Kb
  • LPC: Ligand-Protein Contacts for 3LY5
  • CSU: Contacts of Structural Units for 3LY5
  • Structure Factors (168 Kb)
  • Retrieve 3LY5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3LY5 from S2C, [Save to disk]
  • Re-refined 3ly5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3LY5 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 3LY5
  • 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
  • 3D motif for 3LY5, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ly5] [3ly5_B] [3ly5_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3LY5: [DEXDc ] by SMART
  • Other resources with information on 3LY5
  • Community annotation for 3LY5 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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