4YVG Crystal Structure of H. influenzae TrmD in complex with AdoMet date
authors Ito, T., Yokoyama, S.
compound source
symmetry
R_factor
R_Free 0.2005
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.55
ligand SAM enzyme
Gene HI
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD., Ito T, Masuda I, Yoshida K, Goto-Ito S, Sekine S, Suh SW, Hou YM, Yokoyama S, Proc Natl Acad Sci U S A. 2015 Aug 4;112(31):E4197-205. doi:, 10.1073/pnas.1422981112. Epub 2015 Jul 16. PMID:26183229
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (51 Kb) [Save to disk]
  • Biological Unit Coordinates (4yvg.pdb1.gz) 89 Kb
  • LPC: Ligand-Protein Contacts for 4YVG
  • CSU: Contacts of Structural Units for 4YVG
  • Structure Factors (706 Kb)
  • Retrieve 4YVG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4YVG from S2C, [Save to disk]
  • Re-refined 4yvg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4YVG 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 4YVG
  • 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
  • Fold representative 4yvg from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4yvg_A] [4yvg]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4YVG
  • Community annotation for 4YVG at PDBWiki (http://pdbwiki.org)

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