5BYG Dna Binding Protein Dna date Jun 10, 2015
title X-Ray Structure Of Aav2 Obd-Aavs1 Complex 2:1
authors F.N.Musayev, C.R.Escalante
compound source
Molecule: Protein Rep78
Chain: A, B, C, D
Fragment: Unp Residues 1-210
Engineered: Yes
Organism_scientific: Adeno-Associated Virus 2
Organism_common: Aav-2
Organism_taxid: 648242
Strain: Isolate Srivastava1982
Gene: Rep78
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Dna (5'- D(Cptpcpgpgpcpgpcptpcpgpcptpcpgpcptpcpgp 3');
Chain: E, G
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Dna (5'- D(Gpapgpcpgpapgpcpgpapgpcpgpapgpcpgpcpcp 3');
Chain: F, H
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: C 1 2 1
R_factor 0.189 R_Free 0.227
crystal
cell
length a length b length c angle alpha angle beta angle gamma
183.136 79.595 139.502 90.00 98.12 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand CIT, MG enzyme
Primary referenceStructural Insights into the Assembly of the Adeno-Associated Virus Type 2 Rep68 Protein on the Integration site AAVS1., Musayev FN, Zarate-Perez F, Bishop C, Burgner JW 2nd, Escalante CR, J Biol Chem. 2015 Sep 14. pii: jbc.M115.669960. PMID:26370092
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (349 Kb) [Save to disk]
  • Biological Unit Coordinates (5byg.pdb1.gz) 170 Kb
  • Biological Unit Coordinates (5byg.pdb2.gz) 162 Kb
  • LPC: Ligand-Protein Contacts for 5BYG
  • CSU: Contacts of Structural Units for 5BYG
  • Structure Factors (1138 Kb)
  • Retrieve 5BYG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5BYG from S2C, [Save to disk]
  • Re-refined 5byg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5BYG 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 5BYG
  • 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: [5byg_H] [5byg_G] [5byg_A] [5byg_E] [5byg] [5byg_C] [5byg_B] [5byg_F] [5byg_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5BYG
  • Community annotation for 5BYG at PDBWiki (http://pdbwiki.org)

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