3IUY Hydrolase date Aug 31, 2009
title Crystal Structure Of Ddx53 Dead-Box Domain
authors P.Schutz, T.Karlberg, R.Collins, C.H.Arrowsmith, H.Berglund, C.Bo 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: Probable Atp-Dependent Rna Helicase Ddx53
Chain: A, B
Fragment: Unp Residues 204-430, Helicase Atp-Binding Domain
Synonym: Dead Box Protein 53, Dead Box Protein Cage, Cancer Associated Gene Protein, Cancertestis Antigen 26, Ct26;
Ec: 3.6.1.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ddx53, Cage
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) R3 Prare
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic-Bsa4
symmetry Space Group: P 1 21 1
R_factor 0.201 R_Free 0.251
crystal
cell
length a length b length c angle alpha angle beta angle gamma
56.442 61.251 65.787 90.00 96.36 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand AMP, CL 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] (74 Kb) [Save to disk]
  • Biological Unit Coordinates (3iuy.pdb1.gz) 36 Kb
  • Biological Unit Coordinates (3iuy.pdb2.gz) 35 Kb
  • LPC: Ligand-Protein Contacts for 3IUY
  • CSU: Contacts of Structural Units for 3IUY
  • Structure Factors (263 Kb)
  • Retrieve 3IUY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3IUY from S2C, [Save to disk]
  • Re-refined 3iuy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3IUY 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 3IUY
  • 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 3IUY, from MSDmotif at EBI
  • Fold representative 3iuy from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3iuy_B] [3iuy] [3iuy_A]
  • SWISS-PROT database: [Q86TM3]
  • Domain organization of [DDX53_HUMAN] by SWISSPFAM
  • Domain found in 3IUY: [DEXDc ] by SMART
  • Other resources with information on 3IUY
  • Community annotation for 3IUY 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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