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

• PDB DOI: https://doi.org/10.2210/pdb1RCA/pdb

• Classification: HYDROLASE (ENDORIBONUCLEASE)
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 1994-07-18 Released: 1995-09-15 
• Deposition Author(s): Lisgarten, J.N., Palmer, R.A.

---

Experimental Data Snapshot

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

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

• PubMed: 15299807 
• DOI: https://doi.org/10.1107/S0907444995001570
• Primary Citation of Related Structures:  
  1RCA


• 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 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.

---

Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.92 kDa 
• Atom Count: 1,037 
• Modelled Residue Count: 124 
• Deposited Residue Count: 124 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBONUCLEASE A	A	124	Bos taurus	Mutation(s): 0  EC: 3.1.27.5
UniProt
Find proteins for P61823 (Bos taurus) Explore P61823  Go to UniProtKB:  P61823

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CGP	C [auth A], D [auth A]	2'-DEOXYCYTIDINE-2'-DEOXYGUANOSINE-3',5'-MONOPHOSPHATE C19 H25 N8 O10 P OBCJQWSXSLYWHI-GVKYBDNRSA-N
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

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 = 30.5	α = 90
b = 38.7	β = 106.3
c = 53.7	γ = 90

Software Package:

Software Name	Purpose
RESTRAIN	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-09-15 
Deposition Author(s): Lisgarten, J.N., Palmer, R.A.

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