8R5V | pdb_00008r5v

Crystal structure of bovine pancreatic ribonuclease A in complex with [Sp-PS]-mU-dT dinucleotide

• PDB DOI: https://doi.org/10.2210/pdb8R5V/pdb

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


• Deposited: 2023-11-17 Released: 2023-12-06 
• Deposition Author(s): Dolot, R., Jastrzebska, K., Antonczyk, P.
• Funding Organization(s): Polish National Science Centre

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.170 (DCC) 

Starting Model: experimental

Literature

P-Stereodefined morpholino dinucleoside 3',5'-phosphorothioates.

Jastrzebska, K., Antonczyk, P., Dolot, R.

(2024) Org Biomol Chem 22: 8737-8742

• PubMed: 39392463 
• DOI: https://doi.org/10.1039/d4ob01437e
• Primary Citation of Related Structures:  
  8R5V


• PubMed Abstract: 
  

  Here, we present for the first time the synthesis of P-stereodefined morpholino phosphorothioate analogs by using a modified 1,3,2-oxathiaphospholane method (OTP method) and provide valuable structural insights into their stereochemistry. N -(2-Thio-4,4-pentamethylene-1,3,2-oxathiaphospholane) derivatives of morpholino-type nucleosides ( m U-OTPs) were synthesized, separated into pure P-diastereomers and used to prepare P-stereodefined morpholino dinucleoside 3',5'-phosphorothioates.

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Organizational Affiliation: 
• Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry, Sienkiewicza 112, 90-363 Łódź, Poland. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 33.77 kDa 
• Atom Count: 2,413 
• Modeled Residue Count: 243 
• Deposited Residue Count: 300 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease pancreatic	A, B	150	Bos taurus	Mutation(s): 0  EC: 4.6.1.18
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
Y4I (Subject of Investigation/LOI)	C [auth A]	1-[(2~{R},4~{S},5~{R})-5-[[[(2~{R},6~{S})-2-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-6-(hydroxymethyl)morpholin-4-yl]-oxidanyl-phosphinothioyl]oxymethyl]-4-oxidanyl-oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione C19 H26 N5 O10 P S JMOYBKKBBMXKAB-OTRGKRLXSA-N
TF4	D [auth A], E [auth B]	DICHLORO-ACETIC ACID C2 H2 Cl2 O2 JXTHNDFMNIQAHM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.170 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.315	α = 90
b = 32.709	β = 90.069
c = 72.802	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-06 
Deposition Author(s): Dolot, R., Jastrzebska, K., Antonczyk, P.

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Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	2021/43/D/ST4/02433

Revision History  

• Version 1.0: 2023-12-06
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Database references, Structure summary
• Version 1.2: 2024-11-20
  Changes: Database references