1YDG Protein Binding date Dec 23, 2004
title Crystal Structure Of Trp Repressor Binding Protein Wrba
authors J.Gorman, L.Shapiro, S.K.Burley, New York Sgx Research Center F Structural Genomics (Nysgxrc)
compound source
Molecule: Trp Repressor Binding Protein Wrba
Chain: A, B, C, D, E, F, G, H
Engineered: Yes
 Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299
Gene: Dra0214
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
symmetry Space Group: P 32 2 1
R_factor 0.186 R_Free 0.236
crystal
cell
length a length b length c angle alpha angle beta angle gamma
121.611 121.611 207.933 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.00 Å
ligand SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B, H, C, D, G


Primary referenceCrystal structures of the tryptophan repressor binding protein WrbA and complexes with flavin mononucleotide., Gorman J, Shapiro L, Protein Sci. 2005 Dec;14(12):3004-12. PMID:16322580
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (273 Kb) [Save to disk]
  • Biological Unit Coordinates (1ydg.pdb1.gz) 135 Kb
  • Biological Unit Coordinates (1ydg.pdb2.gz) 131 Kb
  • LPC: Ligand-Protein Contacts for 1YDG
  • CSU: Contacts of Structural Units for 1YDG
  • Likely Quarternary Molecular Structure file(s) for 1YDG
  • Structure Factors (933 Kb)
  • Retrieve 1YDG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YDG from S2C, [Save to disk]
  • Re-refined 1ydg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1YDG 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 1YDG
  • 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
  • 3D motif for 1YDG, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ydga_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1ydgb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1ydgc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1ydgd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1ydge_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1ydgf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1ydgg_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1ydgh_, region H [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1ydg_F] [1ydg_B] [1ydg_D] [1ydg_G] [1ydg] [1ydg_H] [1ydg_C] [1ydg_E] [1ydg_A]
  • SWISS-PROT database: [Q9RYU4]
  • Domain organization of [Q9RYU4_DEIRA] by SWISSPFAM
    • Other resources with information on 1YDG
  • Community annotation for 1YDG at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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