5FRM Recombination date Dec 18, 2015
title Crystal Structure Of The Prototype Foamy Virus (Pfv) Intasom Complex With Magnesium And The Insti Xz384 (Compound 4a)
authors D.P.Maskell, V.E.Pye, P.Cherepanov
compound source
Molecule: Pfv Integrase
Chain: A, B
Synonym: Pro-Pol Polyprotein Pr125pol, P87pro-Rt-Rnaseh, P6 P42in, Pfv Integrase;
Engineered: Yes
Organism_scientific: Human Spumaretrovirus
Organism_taxid: 11963
Strain: Hsrv2
Variant: Pol
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_variant: Pc2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pssh6p-Pfv-Infl

Molecule: 5'-D(Aptptpgptpcpaptpgpgpapaptptp Tpcpgpcpa)-3';
Chain: C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-D(Tpgpcpgpapapaptptpcpcpaptpgp 3';
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 41 21 2
R_factor 0.185 R_Free 0.203
crystal
cell
length a length b length c angle alpha angle beta angle gamma
159.737 159.737 123.528 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.58 Å
ligand GOL, MES, MG, SO4, WA5, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceHIV-1 Integrase Strand Transfer Inhibitors with Reduced Susceptibility to Drug Resistant Mutant Integrases., Zhao XZ, Smith SJ, Maskell DP, Metifiot M, Pye VE, Fesen K, Marchand C, Pommier Y, Cherepanov P, Hughes SH, Burke TR Jr, ACS Chem Biol. 2016 Feb 5. PMID:26808478
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (231 Kb) [Save to disk]
  • Biological Unit Coordinates (5frm.pdb1.gz) 438 Kb
  • LPC: Ligand-Protein Contacts for 5FRM
  • CSU: Contacts of Structural Units for 5FRM
  • Structure Factors (2812 Kb)
  • Retrieve 5FRM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5FRM from S2C, [Save to disk]
  • Re-refined 5frm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5FRM 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 5FRM
  • 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
  • Fold representative 5frm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5frm_B] [5frm] [5frm_C] [5frm_D] [5frm_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5FRM
  • Community annotation for 5FRM at PDBWiki (http://pdbwiki.org)

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