2DB3 Hydrolase Rna date Dec 14, 2005
title Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa
authors T.Sengoku, O.Nureki, A.Nakamura, S.Kobayashi, S.Yokoyama, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: 5'-R(Upupupupupupupupupu)-3'
Chain: E, F, G, H
Engineered: Yes
Synthetic: Yes

Molecule: Atp-Dependent Rna Helicase Vasa
Chain: A, B, C, D
Fragment: Residues 200-623
Synonym: Vasa Protein, Antigen Mab46f11
Ec: 3.6.1.3
Engineered: Yes

Organism_scientific: Drosophila Melanogaster
Organism_common: Fruit Fly
Organism_taxid: 7227
Gene: Vasa
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 Codon Plus
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-6p-1
symmetry Space Group: P 1 21 1
R_factor 0.197 R_Free 0.250
crystal
cell
length a length b length c angle alpha angle beta angle gamma
71.050 142.331 130.465 90.00 90.86 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand ANP, MG enzyme Hydrolase E.C.3.6.1.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceStructural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa., Sengoku T, Nureki O, Nakamura A, Kobayashi S, Yokoyama S, Cell. 2006 Apr 21;125(2):287-300. PMID:16630817
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (311 Kb) [Save to disk]
  • Biological Unit Coordinates (2db3.pdb1.gz) 79 Kb
  • Biological Unit Coordinates (2db3.pdb2.gz) 80 Kb
  • Biological Unit Coordinates (2db3.pdb3.gz) 81 Kb
  • Biological Unit Coordinates (2db3.pdb4.gz) 80 Kb
  • LPC: Ligand-Protein Contacts for 2DB3
  • CSU: Contacts of Structural Units for 2DB3
  • Likely Quarternary Molecular Structure file(s) for 2DB3
  • Structure Factors (1006 Kb)
  • Retrieve 2DB3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2DB3 from S2C, [Save to disk]
  • Re-refined 2db3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2DB3 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 2DB3
  • 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 2DB3, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1i2db3, region B:391-573 [Jmol] [rasmolscript] [script source]
  • Fold representative 2db3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2db3_F] [2db3_C] [2db3_E] [2db3_G] [2db3_B] [2db3_H] [2db3] [2db3_A] [2db3_D]
  • SWISS-PROT database: [P09052]
  • Domain organization of [VASA_DROME] by SWISSPFAM
  • Domains found in 2DB3: [DEXDc] [HELICc ] by SMART
  • Other resources with information on 2DB3
  • Community annotation for 2DB3 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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