2ORL

Solution structure of the cytochrome c- para-aminophenol adduct


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 25 
  • Selection Criteria: structure with the lowest interaction energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cytochrome c and organic molecules: solution structure of the p-aminophenol adduct.

Assfalg, M.Bertini, I.Del Conte, R.Giachetti, A.Turano, P.

(2007) Biochemistry 46: 6232-6238

  • DOI: 10.1021/bi7002857
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Protein-protein interactions are driven by specific properties of the molecular surfaces. Cytochrome c, a small electron transfer protein, is involved in a number of biologically relevant interactions with macromolecular partners. Small molecules may ...

    Protein-protein interactions are driven by specific properties of the molecular surfaces. Cytochrome c, a small electron transfer protein, is involved in a number of biologically relevant interactions with macromolecular partners. Small molecules may interfere with such interactions by binding to the surface of cytochrome c. Here we investigated the possibility of weak intermolecular interactions between reduced cytochrome c and a library of 325 small molecules, using WaterLOGSY NMR spectroscopy. Specific binding was found for p-aminophenol. The solution structure of the p-aminophenol-cytochrome c adduct was determined using a combination of in silico tools and NMR-based restraints. The ligand interacts in a specific binding site on the protein surface through a combination of stacking and H-bond interactions. Small but meaningful rearrangements of the solvent-exposed side chains are observed upon ligand binding and contribute to the stabilization of the complex.


    Organizational Affiliation

    ProtEra srl, viale delle idee 22, 50019 Sesto Fiorentino, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c iso-1
A
108Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 1 
Gene Names: CYC1
Find proteins for P00044 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CYC1
Go to UniProtKB:  P00044
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4NL
Query on 4NL

Download SDF File 
Download CCD File 
A
4-AMINOPHENOL
C6 H7 N O
PLIKAWJENQZMHA-UHFFFAOYSA-N
 Ligand Interaction
HEC
Query on HEC

Download SDF File 
Download CCD File 
A
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 25 
  • Selection Criteria: structure with the lowest interaction energy 
  • Olderado: 2ORL Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance