1VBY

Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U mutaion, and Mn2+ bound

Structural Biology Knowledgebase: 1VBY SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.284
  • R-Value Work: 0.239

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1VBY

Classification: TRANSLATION / RNA

Total Structure Weight: 36099.10


Macromolecule Entities
Molecule Chains Length Organism Details
U1 small nuclear ribonucleoprotein A A 100 Homo sapiens Fragment: U1A_RBD(residues 1-100)
Mutation: Y31H, Q36R
Gene Name(s): SNRPA Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
Hepatitis Delta virus ribozyme B 76 synthetic

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MN
Query on MN

B MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.284
  • R-Value Work: 0.239
  • Space Group: H 3 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 108.59 α = 90.00
b = 108.59 β = 90.00
c = 190.52 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-03-03
  • Released Date: 2004-05-18
  • Deposition author(s): Ke, A., Zhou, K., Ding, F., Cate, J.H.D., Doudna, J.A.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4