1RND

NEWLY OBSERVED BINDING MODE IN PANCREATIC RIBONUCLEASE

• PDB DOI: https://doi.org/10.2210/pdb1RND/pdb

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


• Deposited: 1991-10-21 Released: 1994-01-31 
• Deposition Author(s): Aguilar, C.F., Thomas, P.J., Mills, A., Moss, D.S., Palmer, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Observed: 0.190 

Literature

Newly observed binding mode in pancreatic ribonuclease.

Aguilar, C.F., Thomas, P.J., Mills, A., Moss, D.S., Palmer, R.A.

(1992) J Mol Biol 224: 265-267

• PubMed: 1548704 
• DOI: https://doi.org/10.1016/0022-2836(92)90589-c
• Primary Citation of Related Structures:  
  1RNC, 1RND


• PubMed Abstract: 
  

  Dinucleotides containing guanine, when soaked into crystals of bovine pancreatic ribonuclease, have been found to bind in an unexpected manner, quite unlike interpretations of earlier X-ray diffraction studies. This finding has prompted a reexamination of three mononucleotide-RNase complexes from this laboratory resulting in a re-interpretation of the complex that involved a guanine mononucleotide.

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Organizational Affiliation: 

Crystallography Department, Birkbeck College, University of London, U.K.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.15 kDa 
• Atom Count: 1,058 
• 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 (PDB Primary Data), 4.6.1.18 (UniProt)
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
DGP	C [auth A]	2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE C10 H14 N5 O7 P LTFMZDNNPPEQNG-KVQBGUIXSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Observed: 0.190 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.34	α = 90
b = 38.19	β = 105.9
c = 53.37	γ = 90

Software Package:

Software Name	Purpose
RESTRAIN	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-01-31 
Deposition Author(s): Aguilar, C.F., Thomas, P.J., Mills, A., Moss, D.S., Palmer, R.A.

Revision History  

• Version 1.0: 1994-01-31
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.4: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary