1DFU CRYSTAL STRUCTURE OF E.COLI RIBOSOMAL PROTEIN L25 COMPLEXED WITH A 5S RRNA FRAGMENT AT 1.8 A RESOLUTION date
authors Lu, M., Steitz, T.A.
compound source
symmetry
R_factor
R_Free 0.2250000
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.80
ligand MG enzyme
related structures by homologous chain: 1D6K
Gene
Ontology
ChainFunctionProcessComponent
P


Primary referenceStructure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-A resolution., Lu M, Steitz TA, Proc Natl Acad Sci U S A 2000 Feb 29;97(5):2023-8. PMID:10696113
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (42 Kb) [Save to disk]
  • Biological Unit Coordinates (1dfu.pdb1.gz) 37 Kb
  • LPC: Ligand-Protein Contacts for 1DFU
  • CSU: Contacts of Structural Units for 1DFU
  • Likely Quarternary Molecular Structure file(s) for 1DFU
  • Structure Factors (210 Kb)
  • Retrieve 1DFU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DFU from S2C, [Save to disk]
  • Re-refined 1dfu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1DFU 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 1DFU
  • 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 1DFU, from MSDmotif at EBI
  • Structure summary from SCOR (Structural Classification of RNA)
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dfup_, region P [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1dfu_N] [1dfu_M] [1dfu] [1dfu_P]
  • SWISS-PROT database: [P68919]
  • Domain organization of [RL25_ECOLI] by SWISSPFAM
  • Other resources with information on 1DFU
  • Community annotation for 1DFU at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Domain movements in 1DFU from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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