1LWL

Crystal Structure of Cytochrome P450-cam with a Fluorescent Probe D-8-Ad (Adamantane-1-carboxylic acid-5-dimethylamino-naphthalene-1-sulfonylamino-octyl-amide)

• PDB DOI: https://doi.org/10.2210/pdb1LWL/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-05-31 Released: 2002-12-18 
• Deposition Author(s): Dunn, A.R., Hays, A.M., Goodin, D.B., Stout, C.D., Chiu, R., Winkler, J.R., Gray, H.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.247 
• R-Value Work: 0.202 
• R-Value Observed: 0.247 

Literature

Fluorescent probes for cytochrome P450 structural characterization and inhibitor screening

Dunn, A.R., Hays, A.M., Goodin, D.B., Stout, C.D., Chiu, R., Winkler, J.R., Gray, H.B.

(2002) J Am Chem Soc 124: 10254-10255

• PubMed: 12197708 
• DOI: https://doi.org/10.1021/ja0271678
• Primary Citation of Related Structures:  
  1LWL


• PubMed Abstract: 
  

  We have synthesized two luminescent probes (D-4-Ad and D-8-Ad) that target cytochrome P450cam. D-4-Ad luminescence is quenched by Förster energy transfer upon binding (Kd = 0.83 muM) but is restored when the probe is displaced from the active site by camphor. In contrast, D-8-Ad (Kd approximately 0.02 muM) is not displaced from the enzyme, even in the presence of a large excess of camphor. The 2.2 A resolution crystal structure of the D-8-Ad:P450cam complex reveals extensive hydrophobic contacts between the probe and the enzyme, which result from the conformational flexibility of the B', F, and G helices. Probes with properties similar to those of D-4-Ad potentially could be useful for screening P450 inhibitors.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 48.12 kDa 
• Atom Count: 3,582 
• Modelled Residue Count: 404 
• Deposited Residue Count: 417 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450-cam	A	417	Pseudomonas putida	Mutation(s): 0  EC: 1.14.15.1
UniProt
Find proteins for P00183 (Pseudomonas putida) Explore P00183  Go to UniProtKB:  P00183

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
DSO	C [auth A]	ADAMANTANE-1-CARBOXYLIC ACID-5-DIMETHYLAMINO-NAPHTHALENE-1-SULFONYLAMINO-OCTYL-AMIDE C31 H45 N3 O3 S FZFMMSSQQXCBGM-HTNXFJBJSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DSO	Binding MOAD:  1LWL	Kd: 20 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.247 
• R-Value Work: 0.202 
• R-Value Observed: 0.247 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.955	α = 90
b = 75.313	β = 90
c = 93.178	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-12-18 
Deposition Author(s): Dunn, A.R., Hays, A.M., Goodin, D.B., Stout, C.D., Chiu, R., Winkler, J.R., Gray, H.B.

Revision History  

• Version 1.0: 2002-12-18
  Type: Initial release
  
• Version 1.1: 2008-04-28
  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, Refinement description