1P7R | pdb_00001p7r

CRYSTAL STRUCTURE OF REDUCED, CO-EXPOSED COMPLEX OF CYTOCHROME P450CAM WITH (S)-(-)-NICOTINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.284 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.238 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 
    0.274 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1P7R

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Crystallographic Studies on the Complex Behavior of Nicotine Binding to P450cam (CYP101)(dagger).

Strickler, M.Goldstein, B.M.Maxfield, K.Shireman, L.Kim, G.Matteson, D.Jones, J.P.

(2003) Biochemistry 42: 11943-11950

  • DOI: https://doi.org/10.1021/bi034833o
  • Primary Citation Related Structures: 
    1P2Y, 1P7R

  • PubMed Abstract: 

    Crystallographic and spectroscopic studies have been undertaken to characterize the binding behavior of the non-native substrate nicotine in the active site of the monooxygenase hemoprotein cytochrome P450cam. Despite the existence of a theoretical model that is consistent with the observed distribution of monooxygenation products, the crystal structure of the complex indicates that the primary binding mode of nicotine is unproductive. The structure is confirmed by spectral data that indicate direct coordination of substrate pyridine nitrogen with the heme iron. This would be the proper structure for evaluating binding affinity and inhibition. Reduction of the heme from Fe(III) to Fe(II) and introduction of carbon monoxide into crystals of the nicotine-P450cam complex, to simulate molecular oxygen binding, produces reorientation of the nicotine. This orientation is the appropriate one for predicting regioselectivity and the kinetic features of substrate oxidation. While it is not clear that such complicated behavior will be exhibited for other enzyme-substrate interactions, it is clear that a single crystal structure for a given substrate-enzyme interaction may not provide a good description of the binding mode responsible for product formation.


  • Organizational Affiliation
    • Department of Biophysics, University of Rochester, Rochester, New York 14627, USA.

Macromolecule Content 

  • Total Structure Weight: 48.2 kDa 
  • Atom Count: 3,307 
  • Modeled Residue Count: 407 
  • Deposited Residue Count: 420 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome P450-cam420Pseudomonas putidaMutation(s): 0 
Gene Names: CAMC OR CYP101
EC: 1.14.15.1
UniProt
Find proteins for P00183 (Pseudomonas putida)
Explore P00183 
Go to UniProtKB:  P00183
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00183
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



Download:Ideal Coordinates CCD File
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
NCT

Query on NCT



Download:Ideal Coordinates CCD File
C [auth A](S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE
C10 H14 N2
SNICXCGAKADSCV-JTQLQIEISA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.284 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.238 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 0.274 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.455α = 90
b = 63.455β = 90
c = 248.759γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-10-28
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Structure summary