4E7K Recombination Dna date Mar 17, 2012
title Pfv Integrase Target Capture Complex (Tcc-Mn), Freeze-Trappe Strand Transfer, At 3.0 A Resolution
authors G.N.Maertens, P.Cherepanov
compound source
Molecule: Pro-Pol Polyprotein
Chain: A, B
Fragment: Unp Residues 752-1143
Synonym: Pr125pol, Proteasereverse Transcriptaseribonucle P87pro-Rt-Rnaseh, Proteasereverse Transcriptase, P65pro-Rt Ribonuclease H, Rnase H, Integrase, In, P42in;
Ec:,,, 3.4.23.-
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: Target Dna

Synthetic: Yes
Organism_scientific: Synthetic Dna
Organism_taxid: 32630

Molecule: Dna (5'- D(Tpgpcpgpapapaptptpcpcpaptpgpapcpa)-3');
Chain: D
Engineered: Yes
Other_details: Viral Dna

Synthetic: Yes
Organism_scientific: Synthetic Dna
Organism_taxid: 32630

Molecule: Dna (5'- D(Cpcpcpgpapgpgpcpapcpgptpgpcptpapgpcpap Gpcpcptpcpgpgpg)-3');
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Dna
Organism_taxid: 32630
symmetry Space Group: P 41 21 2
R_factor 0.245 R_Free 0.289
length a length b length c angle alpha angle beta angle gamma
163.914 163.914 129.675 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.02 Å
ligand MN, PGE, SO4, ZN enzyme Transferase E.C. BRENDA
A, B

Primary reference3'-Processing and strand transfer catalysed by retroviral integrase in crystallo., Hare S, Maertens GN, Cherepanov P, EMBO J. 2012 May 11. doi: 10.1038/emboj.2012.118. PMID:22580823
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (116 Kb) [Save to disk]
  • Biological Unit Coordinates (4e7k.pdb1.gz) 213 Kb
  • LPC: Ligand-Protein Contacts for 4E7K
  • CSU: Contacts of Structural Units for 4E7K
  • Structure Factors (267 Kb)
  • Retrieve 4E7K in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4E7K from S2C, [Save to disk]
  • Re-refined 4e7k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4E7K 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 4E7K
  • 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 4E7K, from MSDmotif at EBI
  • Fold representative 4e7k from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4e7k_D] [4e7k] [4e7k_C] [4e7k_T] [4e7k_A] [4e7k_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4E7K
  • Community annotation for 4E7K at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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