2XBM Rna Binding Protein date Apr 13, 2010
title Crystal Structure Of The Dengue Virus Methyltransferase Boun 5'-Capped Octameric Rna
authors L.J.Yap, D.H.Luo, K.Y.Chung, S.P.Lim, C.Bodenreider, C.Noble, P.Y. J.Lescar
compound source
Molecule: Nonstructural Protein Ns5
Chain: A, B, C, D
Fragment: Methyltransferase, Residues 2491-2753
Synonym: Dengue Virus Methyltransferase
Organism_scientific: Dengue Virus
Organism_taxid: 12637

Molecule: 5'-(G3apgpapapcpcpupgpa)-3'
Chain: E, F
Synonym: Capped Rna

Synthetic: Yes
symmetry Space Group: P 32
R_factor 0.204 R_Free 0.231
crystal
cell
length a length b length c angle alpha angle beta angle gamma
137.543 137.543 109.385 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.90 Å
ligand G3A, GOL, SAH, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceCrystal structure of the dengue virus methyltransferase bound to a 5'-capped octameric RNA., Yap LJ, Luo D, Chung KY, Lim SP, Bodenreider C, Noble C, Shi PY, Lescar J, PLoS One. 2010 Sep 17;5(9). pii: e12836. PMID:20862256
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (386 Kb) [Save to disk]
  • Biological Unit Coordinates (2xbm.pdb1.gz) 190 Kb
  • Biological Unit Coordinates (2xbm.pdb2.gz) 191 Kb
  • LPC: Ligand-Protein Contacts for 2XBM
  • CSU: Contacts of Structural Units for 2XBM
  • Structure Factors (705 Kb)
  • Retrieve 2XBM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2XBM from S2C, [Save to disk]
  • Re-refined 2xbm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2XBM 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 2XBM
  • 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 2XBM, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2xbm_D] [2xbm] [2xbm_B] [2xbm_A] [2xbm_F] [2xbm_E] [2xbm_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 2XBM
  • Community annotation for 2XBM 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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