3OYD Recombination,Viral Protein Dna date Sep 23, 2010
title Crystal Structure Of The Prototype Foamy Virus (Pfv) Intasom Complex With Magnesium And The Insti Gs9160
authors S.Hare, P.Cherepanov
compound source
Molecule: Pfv Integrase
Chain: A, B
Fragment: Unp Residues 752 To 1143
Synonym: P42in
Engineered: Yes
Organism_scientific: Human Spumaretrovirus
Organism_common: Sfvcpz(Hu)
Organism_taxid: 11963
Strain: Hsrv2
Gene: Pol
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Pc2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pssh6p-Pfv-Infl

Molecule: Dna (5'- D(Aptptpgptpcpaptpgpgpapaptptptpcpgpcpa)
Chain: C
Engineered: Yes
Other_details: 19 Nucleotide Preprocessed Pfv Donor Dna (No Transferred Strand);

Synthetic: Yes
Other_details: Donor Dna Non-Transferred Strand

Molecule: Dna (5'- D(Tpgpcpgpapapaptptpcpcpaptpgpapcpa)-3');
Chain: D
Engineered: Yes
Other_details: 17 Nucleotide Preprocessed Pfv Donor Dna (Tr Strand)

Synthetic: Yes
Other_details: Donor Dna Transferred Strand
symmetry Space Group: P 41 21 2
R_factor 0.207 R_Free 0.234
crystal
cell
length a length b length c angle alpha angle beta angle gamma
159.530 159.530 123.580 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.54 Å
ligand GOL, MG, NH4, SO4, ZN, ZZV enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceMolecular mechanisms of retroviral integrase inhibition and the evolution of viral resistance., Hare S, Vos AM, Clayton RF, Thuring JW, Cummings MD, Cherepanov P, Proc Natl Acad Sci U S A. 2010 Oct 28. PMID:21030679
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (119 Kb) [Save to disk]
  • Biological Unit Coordinates (3oyd.pdb1.gz) 218 Kb
  • LPC: Ligand-Protein Contacts for 3OYD
  • CSU: Contacts of Structural Units for 3OYD
  • Structure Factors (744 Kb)
  • Retrieve 3OYD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3OYD from S2C, [Save to disk]
  • Re-refined 3oyd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3OYD 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 3OYD
  • 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 3OYD, from MSDmotif at EBI
  • Fold representative 3oyd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3oyd_D] [3oyd_B] [3oyd] [3oyd_C] [3oyd_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3OYD
  • Community annotation for 3OYD 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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