1VP3

VACCINIA VIRUS PROTEIN VP39 IN COMPLEX WITH S-ADENOSYLHOMOCYSTEINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Specific protein recognition of an mRNA cap through its alkylated base.

Hodel, A.E.Gershon, P.D.Shi, X.Wang, S.M.Quiocho, F.A.

(1997) Nat Struct Biol 4: 350-354

  • DOI: 10.1038/nsb0597-350
  • Primary Citation of Related Structures:  
    2VP3, 1V39, 1VP9, 1VP3, 1P39

  • PubMed Abstract: 
  • The specific binding of N7-methylguanine cap analogues to the RNA methyltransferase VP39 was observed through X-ray crystallography, providing a prototypical structure for a complex between a protein and an mRNA 5' cap.


    Related Citations: 
    • The 1.85 A Structure of Vaccinia Protein Vp39: A Bifunctional Enzyme that Participates in the Modification of Both Mrna Ends
      Hodel, A.E., Gershon, P.D., Shi, X., Quiocho, F.A.
      (1996) Cell 85: 247

    Organizational Affiliation

    Finsen Laboratory, Rigshospitalet, Copenhagen Biocenter, Ole Maaløes Vej 5, DK-2200 Copenhagen North, Denmark; Biotech Research and Innovation Centre, Copenhagen Biocenter, Ole Maaløes Vej 5, DK-2200 Copenhagen North, Denmark; Danish-Chinese Centre for Proteases and Cancer. Electronic address: m-ploug@finsenlab.dk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VP39A348Vaccinia virus WRMutation(s): 0 
Gene Names: PAPSVACWR095J3R
EC: 2.7.7.19 (PDB Primary Data), 2.1.1.57 (UniProt)
UniProt
Find proteins for P07617 (Vaccinia virus (strain Western Reserve))
Explore P07617 
Go to UniProtKB:  P07617
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH (Subject of Investigation/LOI)
Query on SAH

Download Ideal Coordinates CCD File 
B [auth A]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.6α = 90
b = 67.3β = 117.3
c = 79.6γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-09-17
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model