3L2Q Recombination Dna date Dec 15, 2009
title Crystal Structure Of The Prototype Foamy Virus (Pfv) Intasome In Apo Form
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 0.197 R_Free 0.221
length a length b length c angle alpha angle beta angle gamma
158.250 158.250 124.750 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.25 Å
ligand GOL, 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] (179 Kb) [Save to disk]
  • Biological Unit Coordinates (3l2q.pdb1.gz) 339 Kb
  • LPC: Ligand-Protein Contacts for 3L2Q
  • CSU: Contacts of Structural Units for 3L2Q
  • Structure Factors (1393 Kb)
  • Retrieve 3L2Q in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3L2Q from S2C, [Save to disk]
  • Re-refined 3l2q structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3L2Q 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 3L2Q
  • 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 3L2Q, from MSDmotif at EBI
  • Fold representative 3l2q from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3l2q_D] [3l2q_A] [3l2q] [3l2q_B] [3l2q_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3L2Q
  • Community annotation for 3L2Q 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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