3POV Dna Binding Protein Dna date Nov 23, 2010
title Crystal Structure Of A Sox-Dna Complex
authors C.Bagneris, T.E.Barrett
compound source
Molecule: Orf 37
Chain: A
Engineered: Yes
Organism_scientific: Human Herpesvirus 8 Type M
Organism_taxid: 435895
Gene: Orf37
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Star
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Petm6t1

Molecule: Dna (5'- D(Gpgpgpaptpcpcptpcpcpcpapgptpcpgpapcpc)
Chain: C
Engineered: Yes

Synthetic: Yes
Other_details: Dna Synthesised By Eurogentec

Molecule: Dna (5'- D(Gpgptpcpgpapcptpapgpgpapgpgpaptpcpcpc)
Chain: D
Engineered: Yes

Synthetic: Yes
Other_details: Dna Synthesised By Eurogentec
symmetry Space Group: P 21 21 21
R_factor 0.207 R_Free 0.264
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.520 67.660 174.560 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand FMT, MG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of a KSHV-SOX-DNA complex: insights into the molecular mechanisms underlying DNase activity and host shutoff., Bagneris C, Briggs LC, Savva R, Ebrahimi B, Barrett TE, Nucleic Acids Res. 2011 Jul;39(13):5744-56. Epub 2011 Mar 17. PMID:21421561
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (186 Kb) [Save to disk]
  • Biological Unit Coordinates (3pov.pdb1.gz) 178 Kb
  • LPC: Ligand-Protein Contacts for 3POV
  • CSU: Contacts of Structural Units for 3POV
  • Structure Factors (1189 Kb)
  • Retrieve 3POV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3POV from S2C, [Save to disk]
  • Re-refined 3pov structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3POV 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 3POV
  • 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 3POV, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3pov_D] [3pov_A] [3pov_C] [3pov]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3POV
  • Community annotation for 3POV at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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