5YBD Dna Binding Protein date Sep 04, 2017
title X-Ray Structure Of Ets Domain Of Ergp55 In Complex With E74d
authors A.K.Saxena, S.P.Gangwar
compound source
Molecule: Transcriptional Regulator Erg
Chain: A, X
Fragment: Ets Domain, Unp Residues 317-406
Synonym: Transforming Protein Erg
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Erg
Expression_system: Enterobacteria Phage L1
Expression_system_taxid: 268588
Expression_system_strain: Bl21
Expression_system_variant: De3
Expression_system_cell: Homo Sapiens
Expression_system_vector_type: Bacterial Expression
Expression_system_plasmid: Pet21a(+)

Molecule: Dna (5'-D(Papcpcpgpgpapapgpt)-3')
Chain: B, Y
Engineered: Yes

Synthetic: Yes
Organism_scientific: Drosophila Saltans
Organism_taxid: 7273

Molecule: Dna (5'-D(Pcpapcptptpcpcpgpgpt)-3')
Chain: C, Z
Engineered: Yes

Synthetic: Yes
Organism_scientific: Drosophila Adunca
Organism_taxid: 46893
symmetry Space Group: C 2 2 21
R_factor 0.204 R_Free 0.282
length a length b length c angle alpha angle beta angle gamma
39.279 233.871 80.524 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.77 Å
A, X

Primary referenceComparative structure analysis of the ETSi domain of ERG3 and its complex with the E74 promoter DNA sequence., Sharma R, Gangwar SP, Saxena AK, Acta Crystallogr F Struct Biol Commun. 2018 Oct 1;74(Pt 10):656-663. doi:, 10.1107/S2053230X1801110X. Epub 2018 Sep 21. PMID:30279318
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (104 Kb) [Save to disk]
  • Biological Unit Coordinates (5ybd.pdb1.gz) 50 Kb
  • Biological Unit Coordinates (5ybd.pdb2.gz) 50 Kb
  • CSU: Contacts of Structural Units for 5YBD
  • Structure Factors (68 Kb)
  • Retrieve 5YBD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5YBD from S2C, [Save to disk]
  • View 5YBD 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 5YBD
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5ybd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ybd_A] [5ybd_B] [5ybd_Y] [5ybd_X] [5ybd_Z] [5ybd_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5YBD
  • Community annotation for 5YBD at PDBWiki (http://pdbwiki.org)

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