3OYA Recombination,Viral Protein Dna date Sep 23, 2010
title Crystal Structure Of The Prototype Foamy Virus (Pfv) Intasom Complex With Magnesium And Raltegravir At 2.65 Resolution
authors S.Hare, P.Cherepanov
compound source
Molecule: Pfv Integrase
Chain: A, B
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 0.205 R_Free 0.228
crystal
cell
length a length b length c angle alpha angle beta angle gamma
159.755 159.755 124.139 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.65 Å
ligand GOL, MG, NH4, RLT, SO4, ZN enzyme
note 3OYA (Molecule of the Month:pdb135)supersedes 3L2T
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 (3oya.pdb1.gz) 217 Kb
  • LPC: Ligand-Protein Contacts for 3OYA
  • CSU: Contacts of Structural Units for 3OYA
  • Structure Factors (659 Kb)
  • Retrieve 3OYA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3OYA from S2C, [Save to disk]
  • Re-refined 3oya structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3OYA 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 3OYA
  • 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 3OYA, from MSDmotif at EBI
  • Fold representative 3oya from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3oya_B] [3oya_D] [3oya_C] [3oya] [3oya_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3OYA
  • Community annotation for 3OYA 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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