1Z6D

Ribonuclease A- IMP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The binding of IMP to Ribonuclease A

Hatzopoulos, G.N.Leonidas, D.D.Kardakaris, R.Kobe, J.Oikonomakos, N.G.

(2005) Febs J. 272: 3988-4001

  • DOI: 10.1111/j.1742-4658.2005.04822.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The binding of inosine 5' phosphate (IMP) to ribonuclease A has been studied by kinetic and X-ray crystallographic experiments at high (1.5 A) resolution. IMP is a competitive inhibitor of the enzyme with respect to C>p and binds to the catalytic cle ...

    The binding of inosine 5' phosphate (IMP) to ribonuclease A has been studied by kinetic and X-ray crystallographic experiments at high (1.5 A) resolution. IMP is a competitive inhibitor of the enzyme with respect to C>p and binds to the catalytic cleft by anchoring three IMP molecules in a novel binding mode. The three IMP molecules are connected to each other by hydrogen bond and van der Waals interactions and collectively occupy the B1R1P1B2P0P(-1) region of the ribonucleolytic active site. One of the IMP molecules binds with its nucleobase in the outskirts of the B2 subsite and interacts with Glu111 while its phosphoryl group binds in P1. Another IMP molecule binds by following the retro-binding mode previously observed only for guanosines with its nucleobase at B1 and the phosphoryl group in P(-1). The third IMP molecule binds in a novel mode towards the C-terminus. The RNase A-IMP complex provides structural evidence for the functional components of subsite P(-1) while it further supports the role inferred by other studies to Asn71 as the primary structural determinant for the adenine specificity of the B2 subsite. Comparative structural analysis of the IMP and AMP complexes highlights key aspects of the specificity of the base binding subsites of RNase A and provides a structural explanation for their potencies. The binding of IMP suggests ways to develop more potent inhibitors of the pancreatic RNase superfamily using this nucleotide as the starting point.


    Organizational Affiliation

    Institute of Organic & Pharmaceutical Chemistry, The National Hellenic Research Foundation, Athens, Greece.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease pancreatic
A, B
124Bos taurusMutation(s): 0 
Gene Names: RNASE1 (RNS1)
EC: 4.6.1.18
Find proteins for P61823 (Bos taurus)
Go to Gene View: RNASE1
Go to UniProtKB:  P61823
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IMP
Query on IMP

Download SDF File 
Download CCD File 
A, B
INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IMPKi: 4600000 nM BINDINGMOAD
IMPKi: 4600000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 100.032α = 90.00
b = 32.692β = 90.59
c = 72.474γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
MAR345data collection
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-08-16
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description