2Z4U Hydrolase date Jun 26, 2007
title Crystal Structure Of Wild Type Pd-L4 From Phytolacca Dioica
authors A.Ruggiero, R.Berisio
compound source
Molecule: Ribosome-Inactivating Protein Pd-L4
Chain: A
Synonym: Rrna N- Glycosidase Pd-L3pd-L4
Ec: 3.2.2.22
 Organism_scientific: Phytolacca Dioica
Organism_taxid: 29725
symmetry Space Group: P 21 21 21
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
43.521 58.813 98.774 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.10 Å
ligand EDO enzyme Hydrolase E.C.3.2.2.22 BRENDA
note 2Z4U is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A
  • toxin activity


    • Primary referenceAtomic resolution (1.1 A) structure of the ribosome-inactivating protein PD-L4 from Phytolacca dioica L. leaves., Ruggiero A, Chambery A, Maro AD, Parente A, Berisio R, Proteins. 2007 Oct 26;71(1):8-15. PMID:17963235
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (108 Kb) [Save to disk]
  • Biological Unit Coordinates (2z4u.pdb1.gz) 105 Kb
  • LPC: Ligand-Protein Contacts for 2Z4U
  • CSU: Contacts of Structural Units for 2Z4U
  • Likely Quarternary Molecular Structure file(s) for 2Z4U
  • Structure Factors (922 Kb)
  • Retrieve 2Z4U in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2Z4U from S2C, [Save to disk]
  • Re-refined 2z4u structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2Z4U 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 2Z4U
  • 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 2Z4U, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2z4u_A] [2z4u]
  • SWISS-PROT database: [P84854]
  • Domain organization of [RIPL2_PHYDI] by SWISSPFAM
    • Other resources with information on 2Z4U
  • Community annotation for 2Z4U 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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