3OYM Recombination,Viral Protein Dna date Sep 23, 2010
title Crystal Structure Of The Pfv N224h Mutant Intasome Bound To
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 0.197 R_Free 0.228
crystal
cell
length a length b length c angle alpha angle beta angle gamma
158.050 158.050 122.160 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.02 Å
ligand GOL, HEZ, MN, NH4, SO4, ZN 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] (126 Kb) [Save to disk]
  • Biological Unit Coordinates (3oym.pdb1.gz) 233 Kb
  • LPC: Ligand-Protein Contacts for 3OYM
  • CSU: Contacts of Structural Units for 3OYM
  • Structure Factors (1408 Kb)
  • Retrieve 3OYM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3OYM from S2C, [Save to disk]
  • Re-refined 3oym structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3OYM 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 3OYM
  • 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 3OYM, from MSDmotif at EBI
  • Fold representative 3oym from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3oym_B] [3oym_D] [3oym] [3oym_C] [3oym_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3OYM
  • Community annotation for 3OYM 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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