PDBsum entry 1ras

Go to PDB code: 
protein ligands links
Hydrolase(nucleic acid,RNA) PDB id
Jmol PyMol
Protein chain
123 a.a. *
Waters ×100
* Residue conservation analysis
PDB id:
Name: Hydrolase(nucleic acid,RNA)
Title: Crystal structure of a fluorescent derivative of rnase a
Structure: Ribonuclease a. Chain: a. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas
Biol. unit: Dimer (from PQS)
1.70Å     R-factor:   0.203    
Authors: S.Baudet-Nessler,M.Jullien,M.-P.Crosio,J.Janin
Key ref:
S.Baudet-Nessler et al. (1993). Crystal structure of a fluorescent derivative of RNase A. Biochemistry, 32, 8457-8464. PubMed id: 8357795 DOI: 10.1021/bi00084a010
02-Mar-93     Release date:   31-Oct-93    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic
150 a.a.
123 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - 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     nucleic acid phosphodiester bond hydrolysis   3 terms 
  Biochemical function     nucleic acid binding     7 terms  


DOI no: 10.1021/bi00084a010 Biochemistry 32:8457-8464 (1993)
PubMed id: 8357795  
Crystal structure of a fluorescent derivative of RNase A.
S.Baudet-Nessler, M.Jullien, M.P.Crosio, J.Janin.
The crystal structure of RNase A chemically modified with the fluorescent probe, N-[[(iodoacetyl)-amino]ethyl]-5-naphthylamine-1-sulfonic acid (1,5-IAENS), has been solved and refined to high resolution. It yields information on the mode of binding, the mobility of a probe commonly used in spectroscopic studies, and anion binding sites in RNase A. Trigonal crystals of the fluorescent derivative grown in sodium or cesium chloride and ammonium sulfate, pH 5.1, were nearly isomorphous with those of a semisynthetic RNase [DeMel, et al. (1992) J. Biol. Chem. 267, 247-256]. Refinement starting from semisynthetic RNase led to a model with R = 20% against 1.7-A diffraction data from crystals in ammonium sulfate and another model with R = 17% against 1.9-A data taken in the presence of 3 M NaCl. The second model contains three chloride ions: one is at the active site, and the other two are at molecular interfaces. Otherwise, the two models are very similar. The fluorophore has very little effect on the protein conformation. It is found to be covalently attached to the active site His-12 with the naphthyl group stacked on the imidazole ring of His-119. It remains largely accessible to solvent and in a polar environment on the protein surface, even though the fluorescence emission spectrum is blue shifted as it is in nonpolar solvents.

Literature references that cite this PDB file's key reference

  PubMed id Reference
16150733 W.L.Vos, R.B.Koehorst, R.B.Spruijt, and M.A.Hemminga (2005).
Membrane-bound conformation of M13 major coat protein: a structure validation through FRET-derived constraints.
  J Biol Chem, 280, 38522-38527.  
15347690 J.Silhan, V.Obsilova, J.Vecer, P.Herman, M.Sulc, J.Teisinger, and T.Obsil (2004).
14-3-3 protein C-terminal stretch occupies ligand binding groove and is displaced by phosphopeptide binding.
  J Biol Chem, 279, 49113-49119.  
11170442 D.D.Root, and K.Wang (2001).
High-affinity actin-binding nebulin fragments influence the actoS1 complex.
  Biochemistry, 40, 1171-1186.  
8973167 A.A.Fedorov, D.Joseph-McCarthy, E.Fedorov, D.Sirakova, I.Graf, and S.C.Almo (1996).
Ionic interactions in crystalline bovine pancreatic ribonuclease A.
  Biochemistry, 35, 15962-15979.
PDB codes: 1rno 1rnq 1rnw 1rnx 1rny 1rnz
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.