5DSD Viral Protein date Sep 17, 2015
title The Crystal Structure Of The C-Terminal Domain Of Ebola (Bun Nucleoprotein
authors L.Baker, K.B.Handing, D.Utepbergenov, U.Derewenda, Z.S.Derewenda
compound source
Molecule: Nucleoprotein
Chain: A
Fragment: C-Terminal Domain (Unp Residues 641-739)
Engineered: Yes
Organism_scientific: Bundibugyo Virus
Organism_taxid: 565995
Gene: Np, Dh33_45404gpnp
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3) Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Parallel1-Mbphis
symmetry Space Group: P 64 2 2
R_factor 0.168 R_Free 0.203
crystal
cell
length a length b length c angle alpha angle beta angle gamma
108.957 108.957 82.736 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.31 Å
ligand CL, GOL enzyme
note 5DSD supersedes 5CIJ
Gene DH33
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceMolecular architecture of the nucleoprotein C-terminal domain from the Ebola and Marburg viruses., Baker LE, Ellena JF, Handing KB, Derewenda U, Utepbergenov D, Engel DA, Derewenda ZS, Acta Crystallogr D Struct Biol. 2016 Jan;72(Pt 1):49-58. doi:, 10.1107/S2059798315021439. Epub 2016 Jan 1. PMID:26894534
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (46 Kb) [Save to disk]
  • Biological Unit Coordinates (5dsd.pdb1.gz) 40 Kb
  • Biological Unit Coordinates (5dsd.pdb2.gz) 79 Kb
  • Biological Unit Coordinates (5dsd.pdb3.gz) 79 Kb
  • LPC: Ligand-Protein Contacts for 5DSD
  • CSU: Contacts of Structural Units for 5DSD
  • Structure Factors (243 Kb)
  • Retrieve 5DSD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5DSD from S2C, [Save to disk]
  • Re-refined 5dsd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5DSD 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 5DSD
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5dsd] [5dsd_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5DSD
  • Community annotation for 5DSD at PDBWiki (http://pdbwiki.org)

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