1RCA

STRUCTURE OF THE CRYSTALLINE COMPLEX OF DEOXYCYTIDYLYL-3',5'-GUANOSINE (3',5'-DCPDG) CO-CRYSTALISED WITH RIBONUCLEASE AT 1.9 ANGSTROMS RESOLUTION. RETROBINDING IN PANCREATIC RNASEA IS INDEPENDENT OF MODE OF INHIBITOR INTROMISSION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Observed: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the crystalline complex of deoxycytidylyl-3',5'-guanosine (3',5'-dCpdG) cocrystallized with ribonuclease at 1.9 A resolution.

Listgarten, J.N.Maes, D.Wyns, L.Aguilar, C.F.Palmer, R.A.

(1995) Acta Crystallogr D Biol Crystallogr 51: 767-771

  • DOI: 10.1107/S0907444995001570
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The X-ray structure of bovine ribonuclease A cocrystallized with the dinucleotide deoxycytidylyl-3',5'-guanosine has been determined at 1.9 A resolution and refined by restrained least squares to R = 0.218 for 7807 reflections. The structure establis ...

    The X-ray structure of bovine ribonuclease A cocrystallized with the dinucleotide deoxycytidylyl-3',5'-guanosine has been determined at 1.9 A resolution and refined by restrained least squares to R = 0.218 for 7807 reflections. The structure established that the recently observed retrobound mode of attachment of substrate analogues cytidylyl-2',5'-guanosine and deoxycytidylyl-3',5'-guanosine found in soaked RNase A crystals is also present in the cocrystallized complex. Retrobinding is thus unlikely to be the result of restrictions imposed by the crystalline environment as the ligands soak into the lattice but rather a phenomenon specific to small nucleotides containing guanine.


    Related Citations: 
    • Newly Observed Binding Mode in Pancreatic Ribonuclease
      Aguilar, C.F., Thomas, P.J., Mills, A., Moss, D.S., Palmer, R.A.
      (1991) J Mol Biol 221: 265
    • The Refined Structure of Ribonuclease-A at 1.45 Angstroms Resolution
      Borkakoti, N., Moss, D.S., Stanford, M.J., Palmer, R.A.
      (1984) J Crystallogr Spectrosc Res 14: 467
    • Ribonuclease-A: Least-Squares Refinement of the Structure at 1.45 Angstroms Resolution
      Borkakoti, N., Moss, D.S., Palmer, R.A.
      (1982) Acta Crystallogr B 38: 2210

    Organizational Affiliation

    Department of Ultrastructure, Institut voor Moleculaire Biologie, Vrije Universiteit Brussel, Sint-Genesius-Ride, Belgium.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBONUCLEASE A
A
124Bos taurusMutation(s): 0 
Gene Names: RNASE1RNS1
EC: 3.1.27.5 (PDB Primary Data), 4.6.1.18 (UniProt)
Find proteins for P61823 (Bos taurus)
Go to UniProtKB:  P61823
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CGP
Query on CGP

Download CCD File 
A
2'-DEOXYCYTIDINE-2'-DEOXYGUANOSINE-3',5'-MONOPHOSPHATE
C19 H25 N8 O10 P
OBCJQWSXSLYWHI-GVKYBDNRSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Observed: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.5α = 90
b = 38.7β = 106.3
c = 53.7γ = 90
Software Package:
Software NamePurpose
RESTRAINrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-09-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance