9JWD | pdb_00009jwd

Crystal structure of RNAs A treated with sodium cyanide

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

  • Deposited: 2024-10-10 Released: 2024-12-04 
  • Deposition Author(s): Ahmad, M.S., Shah, N.
  • Funding Organization(s): Not funded

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 
    0.258 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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Literature

Cyanide mediated conformational changes resulted in the displacement of sulfate ion from the active site of bovine pancreatic ribonuclease A.

Shah, N.Akbar, Z.Ahmad, M.S.

(2024) Biochem Biophys Res Commun 736: 150868-150868

  • DOI: https://doi.org/10.1016/j.bbrc.2024.150868
  • Primary Citation Related Structures: 
    9JWD, 9JWH

  • PubMed Abstract: 

    Ribonuclease A is a major hydrolyzing enzyme involved in the hydrolysis of RNA. The crystals of bovine pancreatic RNase A (bpRNase A) were grown at pH 5.5. The effect of sodium cyanide on bpRNase A was assessed by adding it directly to the crystal containing well. Treating the crystals of bpRNase A with sodium cyanide resulted in the displacement of the sulfate ion from the active site of bpRNase A, while the additional sulfate ion, bound to Ala-4, remained unaffected. The addition of sodium cyanide to bpRNase A crystals did not show change in the secondary structure elements of the enzyme. This study was conducted to check the effect of cyanide on bpRNase A crystals and to displace sulfate ion from its active site.


  • Organizational Affiliation
    • Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan.

Macromolecule Content 

  • Total Structure Weight: 14.03 kDa 
  • Atom Count: 1,069 
  • Modeled Residue Count: 124 
  • Deposited Residue Count: 124 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribonuclease pancreatic124Bos taurusMutation(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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61823
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
(Subject of Investigation/LOI)

Query on SO4



Download:Ideal Coordinates CCD File
G [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
CYN
(Subject of Investigation/LOI)

Query on CYN



Download:Ideal Coordinates CCD File
B [auth A]CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free:  0.258 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.329α = 90
b = 64.329β = 90
c = 64.102γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PROTEUM PLUSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release