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 

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This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1021/bi7002857
  • Primary Citation of Related Structures:  
    2HV4, 2ORL

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c iso-1108Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: CYC1
Find proteins for P00044 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00044 
Go to UniProtKB:  P00044
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00044
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HEC

Download Ideal Coordinates CCD File 
B [auth A]HEME C
C34 H34 Fe N4 O4
Query on 4NL

Download Ideal Coordinates CCD File 
C6 H7 N O
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Data collection, Database references, Derived calculations