429D Rna date Sep 29, 1998
title Crystal Structure Of A Leadzyme; Metal Binding And Implicati Catalysis
authors J.E.Wedekind, D.B.Mckay
compound source
Molecule: Rna (5'-R(Cpgpgpapcpcpgpapgpcpcpapg)
Chain: A, C
Engineered: Yes
Synthetic: Yes

Molecule: Rna (5'-R(Gpcpupgpgpgpapgpupcpc)-3')
Chain: B, D
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 61 2 2
R_factor 0.255 R_Free 0.275
crystal
cell
length a length b length c angle alpha angle beta angle gamma
60.400 60.400 133.100 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.70 Å
ligand MG enzyme
Primary referenceCrystal structure of a lead-dependent ribozyme revealing metal binding sites relevant to catalysis., Wedekind JE, McKay DB, Nat Struct Biol 1999 Mar;6(3):261-8. PMID:10074945
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (24 Kb) [Save to disk]
  • Biological Unit Coordinates (429d.pdb1.gz) 10 Kb
  • Biological Unit Coordinates (429d.pdb2.gz) 10 Kb
  • LPC: Ligand-Protein Contacts for 429D
  • CSU: Contacts of Structural Units for 429D
  • Likely Quarternary Molecular Structure file(s) for 429D
  • Structure Factors (65 Kb)
  • Retrieve 429D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 429D from S2C, [Save to disk]
  • Re-refined 429d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 429D 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 429D
  • 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 429D, from MSDmotif at EBI
  • Structure summary from SCOR (Structural Classification of RNA)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [429d_C] [429d_A] [429d_B] [429d_D] [429d]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 429D
  • Community annotation for 429D 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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