1VBZ Translation Rna date Mar 03, 2004
title Crystal Structure Of The Hepatitis Delta Virus Gemonic Riboz Precursor, With C75u Mutaion, In Ba2+ Solution
authors A.Ke, K.Zhou, F.Ding, J.H.D.Cate, J.A.Doudna
compound source
Molecule: Hepatitis Delta Virus Ribozyme
Chain: B
Engineered: Yes
Mutation: Yes
Synthetic: Yes
Other_details: Rna Occurs From Hapatitis Delta Virus Pathog Vitro Transcription With Puc19;

Molecule: U1 Small Nuclear Ribonucleoprotein A
Chain: A
Fragment: U1a_rbd(Residues 1-100)
Synonym: U1 Snrnp Protein A, U1a Protein, U1-A
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet
symmetry Space Group: H 3 2
R_factor 0.253 R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
108.630 108.630 190.072 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.80 Å
ligand BA enzyme
related structures by homologous chain: 1VBY, 1VC6
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceA conformational switch controls hepatitis delta virus ribozyme catalysis., Ke A, Zhou K, Ding F, Cate JH, Doudna JA, Nature 2004 May 13;429(6988):201-5. PMID:15141216
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (52 Kb) [Save to disk]
  • Biological Unit Coordinates (1vbz.pdb1.gz) 46 Kb
  • LPC: Ligand-Protein Contacts for 1VBZ
  • CSU: Contacts of Structural Units for 1VBZ
  • Likely Quarternary Molecular Structure file(s) for 1VBZ
  • Structure Factors (93 Kb)
  • Retrieve 1VBZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VBZ from S2C, [Save to disk]
  • Re-refined 1vbz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1VBZ 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 1VBZ
  • 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 1VBZ, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1vbza_, region A [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: [1vbz] [1vbz_A] [1vbz_B]
  • SWISS-PROT database: [P09012]
  • Domain organization of [SNRPA_HUMAN] by SWISSPFAM
  • Domain found in 1VBZ: [RRM ] by SMART
  • Other resources with information on 1VBZ
  • Community annotation for 1VBZ at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science