1TD2 Crystal Structure of the PdxY Protein from Escherichia coli date
authors Safo, M.K., Musayev, F.N., Hunt, S., Salvo, M.di., Scarsdale, N., Schirch, V.
compound source
symmetry
R_factor
R_Free 0.246
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.22
ligand PXL, SO4 enzyme
related structures by homologous chain: 1VI9
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structure of the PdxY Protein from Escherichia coli., Safo MK, Musayev FN, Hunt S, di Salvo ML, Scarsdale N, Schirch V, J Bacteriol 2004 Dec;186(23):8074-82. PMID:15547280
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (102 Kb) [Save to disk]
  • Biological Unit Coordinates (1td2.pdb1.gz) 98 Kb
  • LPC: Ligand-Protein Contacts for 1TD2
  • CSU: Contacts of Structural Units for 1TD2
  • Likely Quarternary Molecular Structure file(s) for 1TD2
  • Structure Factors (210 Kb)
  • Retrieve 1TD2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1TD2 from S2C, [Save to disk]
  • Re-refined 1td2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1TD2 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 1TD2
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1TD2, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1td2a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1td2b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1d1td2, region D:163-338 [Jmol] [rasmolscript] [script source]
        - Domain d1m1td2, region D:269-392 [Jmol] [rasmolscript] [script source]
  • Fold representative 1td2 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1td2] [1td2_B] [1td2_A]
  • SWISS-PROT database: [P77150]
  • Domain organization of [PDXY_ECOLI] by SWISSPFAM
  • Other resources with information on 1TD2
  • Community annotation for 1TD2 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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