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PDBsum entry 3euz

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
3euz
Jmol
Contents
Protein chains
119 a.a. *
Ligands
DMF
Waters ×242
* Residue conservation analysis
PDB id:
3euz
Name: Hydrolase
Title: Crystal structure of ribonuclease a in 50% dimethylformamide
Structure: Ribonuclease pancreatic. Chain: a, b. Synonym: rnase 1, rnase a. Ec: 3.1.27.5
Source: Bos taurus. Bovine. Organism_taxid: 9913. Organ: pancreas
Resolution:
1.84Å     R-factor:   0.194     R-free:   0.229
Authors: M.Dechene,G.Wink,M.Smith,P.Swartz,C.Mattos
Key ref:
M.Dechene et al. (2009). Multiple solvent crystal structures of ribonuclease A: An assessment of the method. Proteins, 76, 861-881. PubMed id: 19291738 DOI: 10.1002/prot.22393
Date:
12-Oct-08     Release date:   23-Jun-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic
Seq:
Struc:
150 a.a.
119 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.27.5  - Pancreatic ribonuclease.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in C-P or U-P with 2',3'-cyclic phosphate intermediates.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   3 terms 
  Biochemical function     nucleic acid binding     7 terms  

 

 
DOI no: 10.1002/prot.22393 Proteins 76:861-881 (2009)
PubMed id: 19291738  
 
 
Multiple solvent crystal structures of ribonuclease A: An assessment of the method.
M.Dechene, G.Wink, M.Smith, P.Swartz, C.Mattos.
 
  ABSTRACT  
 
The multiple solvent crystal structures (MSCS) method uses organic solvents to map the surfaces of proteins. It identifies binding sites and allows for a more thorough examination of protein plasticity and hydration than could be achieved by a single structure. The crystal structures of bovine pancreatic ribonuclease A (RNAse A) soaked in the following organic solvents are presented: 50% dioxane, 50% dimethylformamide, 70% dimethylsulfoxide, 70% 1,6-hexanediol, 70% isopropanol, 50% R,S,R-bisfuran alcohol, 70% t-butanol, 50% trifluoroethanol, or 1.0M trimethylamine-N-oxide. This set of structures is compared with four sets of crystal structures of RNAse A from the protein data bank (PDB) and with the solution NMR structure to assess the validity of previously untested assumptions associated with MSCS analysis. Plasticity from MSCS is the same as from PDB structures obtained in the same crystal form and deviates only at crystal contacts when compared to structures from a diverse set of crystal environments. Furthermore, there is a good correlation between plasticity as observed by MSCS and the dynamic regions seen by NMR. Conserved water binding sites are identified by MSCS to be those that are conserved in the sets of structures taken from the PDB. Comparison of the MSCS structures with inhibitor-bound crystal structures of RNAse A reveals that the organic solvent molecules identify key interactions made by inhibitor molecules, highlighting ligand binding hot-spots in the active site. The present work firmly establishes the relevance of information obtained by MSCS. Proteins 2009. (c) 2009 Wiley-Liss, Inc.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Crystallographic water molecules on the surface of RNAse A shown as red spheres. Water molecules from one representative MSCS model are shown on the left. Water molecules superimposed from all 20 MSCS models are shown on the right. This figure was prepared using Pymol (Delano Scientific).
Figure 6.
Figure 6. Organic solvent binding sites on the surface of RNAse A. Ribbon diagram of RNAse A showing the binding sites for organic solvent molecules. The -strands are shown in dark gray and the -helices are shown in purple. Residues 16-22 are colored in salmon. The organic solvent molecules are colored as follows: DIO, red; DMF, purple; DMS, green; HEZ, orange; IPA, blue; RSF, yellow; TBU, cyan; ETF, brown; and TMO, black. Organic solvent binding sites are numbered as in Supporting Information Table sII. The RNAse active site pockets are labeled. This figure was prepared using Pymol (Delano Scientific).
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2009, 76, 861-881) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19788411 J.Walters, C.Pop, F.L.Scott, M.Drag, P.Swartz, C.Mattos, G.S.Salvesen, and A.C.Clark (2009).
A constitutively active and uninhibitable caspase-3 zymogen efficiently induces apoptosis.
  Biochem J, 424, 335-345.
PDB code: 3itn
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