5XP8 Dna Binding Protein date Jun 01, 2017
title Crystal Structure Of T. Thermophilus Argonaute Protein Compl A Bulge 4a5 On The Guide Strand
authors G.Sheng, T.Gogakos, J.Wang, H.Zhao, A.Serganov, S.Juranek, T.Tusch J.D.Patel, Y.Wang
compound source
Molecule: Ttago
Chain: A
Synonym: Uncharacterized Protein
Engineered: Yes
 Organism_scientific: Thermus Thermophilus (Strain Hb27 At 163 Dsm 7039);
Organism_taxid: 262724
Strain: Hb27 Atcc Baa-163 Dsm 7039
Gene: Tt_p0026
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Dna (5'- D(Ptpgpapgpapgptpapgptpapgpgptptpgpt)-3');
Chain: E
Engineered: Yes
Synthetic: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Dna (5'-D(Cpapapcpcaptpapcptpapcpcp 3');
Chain: F
Engineered: Yes
Synthetic: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Dna (5'-D(Apgpt)-3')
Chain: C
Engineered: Yes
Synthetic: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
symmetry Space Group: P 41 3 2
R_factor 0.214 R_Free 0.276
crystal
cell
length a length b length c angle alpha angle beta angle gamma
202.140 202.140 202.140 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.10 Å
ligand MG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes., Sheng G, Gogakos T, Wang J, Zhao H, Serganov A, Juranek S, Tuschl T, Patel DJ, Wang Y, Nucleic Acids Res. 2017 Sep 6;45(15):9149-9163. doi: 10.1093/nar/gkx547. PMID:28911094
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (251 Kb) [Save to disk]
  • Biological Unit Coordinates (5xp8.pdb1.gz) 242 Kb
  • LPC: Ligand-Protein Contacts for 5XP8
  • CSU: Contacts of Structural Units for 5XP8
  • Structure Factors (657 Kb)
  • Retrieve 5XP8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5XP8 from S2C, [Save to disk]
    • View 5XP8 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 5XP8
  • 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: [5xp8_A] [5xp8_C] [5xp8_E] [5xp8_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5XP8
  • Community annotation for 5XP8 at PDBWiki (http://pdbwiki.org)

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