Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.03 kDa 
• Atom Count: 2265 
• Residue Count: 248 
• Unique protein chains: 1

3DJO

Bovine Seminal Ribonuclease uridine 2' phosphate complex

• DOI: 10.2210/pdb3DJO/pdb

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


• Deposited: 2008-06-24 Released: 2009-06-30 
• Deposition Author(s): Dossi, K., Leonidas, D.D., Zographos, S.E., Oikonomakos, N.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.226 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Literature

Mapping the ribonucleolytic active site of bovine seminal ribonuclease. The binding of pyrimidinyl phosphonucleotide inhibitors

Dossi, K., Tsirkone, V.G., Hayes, J.M., Matousek, J., Pouckova, P., Soucek, J., Zadinova, M., Zographos, S.E., Leonidas, D.D.

(2009) Eur J Med Chem 44: 4496-4508

• PubMed: 19643512 
• DOI: 10.1016/j.ejmech.2009.06.039
• Primary Citation of Related Structures:  
  3DJQ, 3DJV, 3DJX, 3DJO, 3DJP


• PubMed Abstract: 
  

Bovine seminal ribonuclease (BS-RNase) is a 27kDa homodimeric enzyme and a member of the pancreatic RNase A superfamily. It is the only RNase with a quaternary structure and it is a mixture of two dimeric forms. In the most abundant form the active site is formed by the swapping of the N-terminal segments. BS-RNase is a potent antitumor agent with severe side effects such as aspermatogenicity, and immunosuppression. As a first step towards the design of potent inhibitors of this enzyme we mapped its active site through the study of the binding of uridine 2'-phosphate (U2'p), uridine 3'-phosphate (U3'p), uridine 5'-diphosphate (UDP), cytidine 3'-phosphate (C3'p), and cytidine 5-phosphate (C5'p), by kinetics, and X-ray crystallography. These phosphonucleotides are potent inhibitors with C3'p being the most potent with a K(i) value of 22 microM. Absorption, distribution, metabolism, and excretion pharmacokinetic property predictions reveal U2'p, U3'p, and C5'p as the most promising with respect to oral bioavailability. In vivo studies on the aspermatogenic effect have shown that C3'p and C5'p inhibit significantly this biological action of BS-RNase.

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Organizational Affiliation: 

Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, 11635 Athens, Greece.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Seminal ribonuclease	A, B	124	Bos taurus	Mutation(s): 0  Gene Names: SRN EC: 3.1.27.5 (PDB Primary Data), 4.6.1.18 (UniProt)
Find proteins for P00669 (Bos taurus) Explore P00669  Go to UniProtKB:  P00669

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U2P	A, B	PHOSPHORIC ACID MONO-[2-(2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-4-HYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-YL] ESTER C9 H13 N2 O9 P HQIDPEYTETUCNF-XVFCMESISA-N
ACT	B	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
U2P	Ki:  40800   nM  Binding MOAD
U2P	Ki:  40800   nM  BindingDB
U2P	Ki :  40800   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.226 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.311	α = 90
b = 59.067	β = 90
c = 82.495	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-06-24 
• Released Date: 2009-06-30 
Deposition Author(s): Dossi, K., Leonidas, D.D., Zographos, S.E., Oikonomakos, N.G.

Revision History 

• Version 1.0: 2009-06-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description