1VBY Translation Rna date Mar 03, 2004
title Crystal Structure Of The Hepatitis Delta Virus Gemonic Ribozyme Precursor, With C75u Mutaion, And Mn2+ Bound
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 Pathogen, In 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 0.239 R_Free 0.284
length a length b length c angle alpha angle beta angle gamma
108.589 108.589 190.519 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.90 Å
ligand MN, NA enzyme
related structures by homologous chain: 1FHT, 1VBZ

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 (1vby.pdb1.gz) 47 Kb
  • LPC: Ligand-Protein Contacts for 1VBY
  • CSU: Contacts of Structural Units for 1VBY
  • Likely Quarternary Molecular Structure file(s) for 1VBY
  • Structure Factors (115 Kb)
  • Retrieve 1VBY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VBY from S2C, [Save to disk]
  • Re-refined 1vby structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1VBY 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 1VBY
  • 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
  • 3D motif for 1VBY, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1vbya_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1vby from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [1vby] [1vby_B] [1vby_A]
  • SWISS-PROT database: [P09012]
  • Domain organization of [SNRPA_HUMAN] by SWISSPFAM
  • Domain found in 1VBY: [RRM ] by SMART
  • Other resources with information on 1VBY
  • Community annotation for 1VBY 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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