3S3M Recombination Inhibitor Dna date May 18, 2011
title Crystal Structure Of The Prototype Foamy Virus (Pfv) Intasom Complex With Magnesium And Dolutegravir (Sgsk1349572)
authors S.Hare, P.Cherepanov
compound source
Molecule: Pfv Integrase
Chain: A, B
Synonym: In, P42in
Ec: 2.7.7.-
Engineered: Yes
Organism_scientific: Human Spumaretrovirus
Organism_common: Sfvcpz(Hu), Human Foamy Virus
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: 5'-D(Aptptpgptpcpaptpgpgpapaptptpt A)-3';
Chain: C
Engineered: Yes
Other_details: 19 Nucleotide Preprocessed Pfv Donor Dna (No Transferred Strand);

Synthetic: Yes
Other_details: Synthesized Oligonucleotide

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

Synthetic: Yes
Other_details: Synthesized Oligonucleotide
symmetry Space Group: P 41 21 2
R_factor 0.206 R_Free 0.232
length a length b length c angle alpha angle beta angle gamma
160.140 160.140 123.430 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.49 Å
ligand DLU, GOL, HEZ, MG, NH4, SO4, ZN enzyme Transferase E.C.2.7.7 BRENDA
A, B

Primary referenceStructural and Functional Analyses of the Second-generation Integrase Strand Transfer Inhibitor Dolutegravir (S/GSK1349572)., Hare S, Smith SJ, Metifiot M, Jaxa-Chamiec A, Pommier Y, Hughes SH, Cherepanov P, Mol Pharmacol. 2011 Jun 30. PMID:21719464
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (119 Kb) [Save to disk]
  • Biological Unit Coordinates (3s3m.pdb1.gz) 218 Kb
  • LPC: Ligand-Protein Contacts for 3S3M
  • CSU: Contacts of Structural Units for 3S3M
  • Structure Factors (2618 Kb)
  • Retrieve 3S3M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3S3M from S2C, [Save to disk]
  • Re-refined 3s3m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3S3M 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 3S3M
  • 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 3S3M, from MSDmotif at EBI
  • Fold representative 3s3m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3s3m] [3s3m_C] [3s3m_B] [3s3m_A] [3s3m_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3S3M
  • Community annotation for 3S3M at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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