3PEY Hydrolase Rna date Oct 27, 2010
title S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
authors B.Montpetit, N.D.Thomsen, K.J.Helmke, M.A.Seeliger, J.M.Berger, K
compound source
Molecule: Atp-Dependent Rna Helicase Dbp5
Chain: A
Synonym: Dead Box Protein 5, Helicase Ca56, Ribonucleic Ac Trafficking Protein 8;
Ec: 3.6.4.13
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
Gene: Dbp5, Rat8, Yor046c
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Ril
Expression_system_vector_type: Plasmid

Molecule: Rna (5'-R(Pupupupupupu)-3')
Chain: B
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.160 R_Free 0.180
crystal
cell
length a length b length c angle alpha angle beta angle gamma
42.136 92.206 104.524 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.40 Å
ligand ADP, BEF, GOL, MG, NO3 enzyme Hydrolase E.C.3.6.4.13 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceA conserved mechanism of DEAD-box ATPase activation by nucleoporins and InsP6 in mRNA export., Montpetit B, Thomsen ND, Helmke KJ, Seeliger MA, Berger JM, Weis K, Nature. 2011 Apr 14;472(7342):238-42. Epub 2011 Mar 27. PMID:21441902
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (156 Kb) [Save to disk]
  • Biological Unit Coordinates (3pey.pdb1.gz) 149 Kb
  • LPC: Ligand-Protein Contacts for 3PEY
  • CSU: Contacts of Structural Units for 3PEY
  • Structure Factors (544 Kb)
  • Retrieve 3PEY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3PEY from S2C, [Save to disk]
  • Re-refined 3pey structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3PEY 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 3PEY
  • 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 3PEY, from MSDmotif at EBI
  • Fold representative 3pey from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3pey] [3pey_A] [3pey_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3PEY: [DEXDc] [HELICc ] by SMART
  • Other resources with information on 3PEY
  • Community annotation for 3PEY 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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