5EJK Transferase Dna date Nov 02, 2015
title Crystal Structure Of The Rous Sarcoma Virus Intasome
authors Z.Yin, K.Shi, S.Banerjee, H.Aihara
compound source
Molecule: Gag-Pro-Pol Polyprotein
Chain: A, B, C, D, E, F, G, H
Fragment: Unp Residues 573-842
Ec: 3.4.23.-,2.7.7.49,2.7.7.7,3.1.26.4,2.7.7.-,3.1.-.-
Engineered: Yes
Mutation: Yes
 Organism_scientific: Rous Sarcoma Virus (Strain Prague C)
Organism_common: Rsv-Prc
Organism_taxid: 11888
Strain: Prague C
Gene: Gag-Pro-Pol
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Rsv Integrase
Chain: I, L
Engineered: Yes
Organism_scientific: Rous Sarcoma Virus (Strain Schmidt-Rup
Organism_taxid: 270623
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'- D(Apaptpgptptpgptpcptptpaptpgpcpapaptpap 3');
Chain: J, M
Engineered: Yes
Synthetic: Yes
Organism_scientific: Rous Sarcoma Virus (Strain Schmidt-Rup
Organism_taxid: 270623

Molecule: Dna (5'-D(Cptptpcptpcptpc)-3')
Chain: K, N
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Dna (5'-D(Apgptpgptpcptpt)-3')
Chain: k, n
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 1 21 1
R_factor 0.254 R_Free 0.295
crystal
cell
length a length b length c angle alpha angle beta angle gamma
124.936 157.854 126.583 90.00 110.94 90.00
method X-Ray Diffractionresolution 3.80 Å
ligand MSE, W, ZN enzyme Hydrolase E.C.3.4.23 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B, H, C, D, G


Primary referenceCrystal structure of the Rous sarcoma virus intasome., Yin Z, Shi K, Banerjee S, Pandey KK, Bera S, Grandgenett DP, Aihara H, Nature. 2016 Feb 18;530(7590):362-6. doi: 10.1038/nature16950. PMID:26887497
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (844 Kb) [Save to disk]
  • Biological Unit Coordinates (5ejk.pdb1.gz) 824 Kb
  • LPC: Ligand-Protein Contacts for 5EJK
  • CSU: Contacts of Structural Units for 5EJK
  • Structure Factors (564 Kb)
  • Retrieve 5EJK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5EJK from S2C, [Save to disk]
  • Re-refined 5ejk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5EJK 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 5EJK
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ejk_L] [5ejk_G] [5ejk_K] [5ejk_I] [5ejk] [5ejk_M] [5ejk_B] [5ejk_J] [5ejk_N] [5ejk_C] [5ejk_n] [5ejk_H] [5ejk_k] [5ejk_A] [5ejk_E] [5ejk_D] [5ejk_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5EJK
  • Community annotation for 5EJK at PDBWiki (http://pdbwiki.org)

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