Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 49.21 kDa 
• Atom Count: 4017 
• Modelled Residue Count: 406 
• Deposited Residue Count: 414 
• Unique protein chains: 1

1QMQ

Optical detection of cytochrome P450 by sensitizer-linked substrates

• PDB DOI: 10.2210/pdb1QMQ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1999-10-05 Released: 2000-10-06 
• Deposition Author(s): Crane, B.R., Dmochowski, I.J., Gray, H.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.226 
• R-Value Work: 0.216 
• R-Value Observed: 0.216 

Literature

Optical Detection of Cytochrome P450 by Sensitizer-Linked Substrates

Dmochowski, I.J., Crane, B.R., Wilker, J.J., Winkler, J.R., Gray, H.B.

(1999) Proc Natl Acad Sci U S A 96: 12987

• PubMed: 10557259 
• DOI: 10.1073/pnas.96.23.12987
• Primary Citation of Related Structures:  
  1QMQ


• PubMed Abstract: 
  

The ability to detect, characterize, and manipulate specific biomolecules in complex media is critical for understanding metabolic processes. Particularly important targets are oxygenases (cytochromes P450) involved in drug metabolism and many disease states, including liver and kidney dysfunction, neurological disorders, and cancer. We have found that Ru photosensitizers linked to P450 substrates specifically recognize submicromolar cytochrome P450(cam) in the presence of other heme proteins. In the P450:Ru-substrate conjugates, energy transfer to the heme dramatically accelerates the Ru-luminescence decay. The crystal structure of a P450(cam):Ru-adamantyl complex reveals access to the active center via a channel whose depth (Ru-Fe distance is 21 A) is virtually the same as that extracted from an analysis of the energy-transfer kinetics. Suitably constructed libraries of sensitizer-linked substrates could be employed to probe the steric and electronic properties of buried active sites.

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Organizational Affiliation: 

Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME P450	A	414	Pseudomonas putida	Mutation(s): 1  Gene Names: cyp101, camC EC: 1.14.15.1
UniProt
Find proteins for P00183 (Pseudomonas putida) Explore P00183  Go to UniProtKB:  P00183

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DRB	C [auth A], D [auth A]	DELTA-BIS(2,2'-BIPYRIDINE)-(5-METHYL-2-2'-BIPYRIDINE)-C9-ADAMANTANE RUTHENIUM (II) C50 H57 N7 O Ru IGSCYCAKHRXAKK-KBBCMHLPSA-N
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
ACT	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.226 
• R-Value Work: 0.216 
• R-Value Observed: 0.216 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.39	α = 90
b = 74.47	β = 90
c = 91.73	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-10-05 
• Released Date: 2000-10-06 
Deposition Author(s): Crane, B.R., Dmochowski, I.J., Gray, H.B.

Revision History  

• Version 1.0: 2000-10-06
  Type: Initial release
  
• Version 1.1: 2012-03-28
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
• Version 2.0: 2018-10-03
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary