3L2V Recombination Dna date Dec 15, 2009
title Crystal Structure Of The Prototype Foamy Virus (Pfv) Intasome In Complex With Manganese And Mk0518 (Raltegravir)
authors S.Hare, S.S.Gupta, P.Cherepanov
compound source
Molecule: Integrase
Chain: A, B
Synonym: In, 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: 5'- D(Aptptpgptpcpaptpgpgpapaptptptptpgptpa) -3';
Chain: C
Engineered: Yes
Other_details: 19 Nucleotide Preprocessed Pfv Donor Dna

Synthetic: Yes

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

Synthetic: Yes
symmetry Space Group: P 41 21 2
R_factor 0.205 R_Free 0.232
length a length b length c angle alpha angle beta angle gamma
158.650 158.650 125.230 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.20 Å
ligand GOL, MN, NH4, RLT, ZN enzyme
A, B

Primary referenceRetroviral intasome assembly and inhibition of DNA strand transfer., Hare S, Gupta SS, Valkov E, Engelman A, Cherepanov P, Nature. 2010 Jan 31. PMID:20118915
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (182 Kb) [Save to disk]
  • Biological Unit Coordinates (3l2v.pdb1.gz) 342 Kb
  • LPC: Ligand-Protein Contacts for 3L2V
  • CSU: Contacts of Structural Units for 3L2V
  • Structure Factors (1468 Kb)
  • Retrieve 3L2V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3L2V from S2C, [Save to disk]
  • Re-refined 3l2v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3L2V 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 3L2V
  • 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 3L2V, from MSDmotif at EBI
  • Fold representative 3l2v from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3l2v_D] [3l2v_C] [3l2v_A] [3l2v_B] [3l2v]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3L2V
  • Community annotation for 3L2V 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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