1QMQ | pdb_00001qmq

Optical detection of cytochrome P450 by sensitizer-linked substrates


Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1QMQ

This is version 2.1 of the entry. See complete history

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

  • DOI: https://doi.org/10.1073/pnas.96.23.12987
  • Primary Citation 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.


  • Organizational Affiliation
    • Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA.

Macromolecule Content 

  • Total Structure Weight: 49.21 kDa 
  • Atom Count: 4,017 
  • Modeled Residue Count: 406 
  • Deposited Residue Count: 414 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CYTOCHROME P450414Pseudomonas putidaMutation(s): 1 
Gene Names: 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
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DRB

Query on DRB



Download:Ideal Coordinates CCD File
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

Query on HEM



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

Query on ACT



Download:Ideal Coordinates CCD File
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 (Depositor) 
  • R-Value Work:  0.216 (Depositor) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.39α = 90
b = 74.47β = 90
c = 91.73γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 2.1: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description