1UYU

Xenon COMPLEX OF wildtype P450CAM FROM PSEUDOMONAS PUTIDA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

A Survey of Active Site Access Channels in Cytochromes P450

Wade, R.C., Winn, P.J., Schlichting, I.

(2004) J.Inorg.Biochem. 98: 1175

  • DOI: 10.1016/j.jinorgbio.2004.02.007

  • PubMed Abstract: 

    • In cytochrome P450s, the active site is situated deep inside the protein next to the heme cofactor, and is often completely isolated from the surrounding solvent. To identify routes by which substrates may enter into and products exit from the active ...

    In cytochrome P450s, the active site is situated deep inside the protein next to the heme cofactor, and is often completely isolated from the surrounding solvent. To identify routes by which substrates may enter into and products exit from the active site, random expulsion molecular dynamics simulations were performed for three cytochrome P450s: CYP101, CYP102A1 and CYP107A1 [J. Mol. Biol. 303 (2000) 797; Proc. Natl. Acad. Sci. USA 99 (2002) 5361]. Amongst the different pathways identified, one pathway was found to be common to all three cytochrome P450s although the mechanism of ligand passage along it was different in each case and apparently adapted to the substrate specificity of the enzyme. Recently, a number of new crystal structures of cytochrome P450s have been solved. Here, we analyse the open channels leading to the active site that these structures reveal. We find that in addition to showing the common pathway, they provide experimental evidence for the existence of three additional channels that were identified by simulation. We also discuss how the location of xenon binding sites in CYP101 suggests a role for one of the pathways identified by molecular dynamics simulations as a route for gaseous species, such as oxygen, to access the active site.

    Related Citations: 
    • High-Resolution Crystal Structure of Cytochrome P450Cam
      Poulos, T.L.,Finzel, B.C.,Howard, A.J.
      (1987) J.Mol.Biol. 195: 687
    • Structural Aspects of Ligand Binding to and Electron Transfer in Bacterial and Fungal P450S
      Pylypenko, O.,Schlichting, I.
      (2004) Annu.Rev.Biochem. 73: 991

    Organizational Affiliation: 

    Molecular and Cellular Modeling, EML Research, Villa Bosch, Schloss-Wolfsbrunnenweg 33, 69118, Heidelberg, Germany. rebecca.wade@eml-r.villa-bosch.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME P450-CAM
A, B
414Pseudomonas putidaMutation(s): 0 
Gene Names: camC (cyp101)
EC: 1.14.15.1
Find proteins for P00183 (Pseudomonas putida)
Go to UniProtKB:  P00183
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K
Download SDF File 
Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CAM
Query on CAM
Download SDF File 
Download CCD File 
A, B
CAMPHOR
C10 H16 O
DSSYKIVIOFKYAU-XCBNKYQSSA-N
 Ligand Interaction
HEM
Query on HEM
Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
XE
Query on XE
Download SDF File 
Download CCD File 
A, B
XENON
Xe
FHNFHKCVQCLJFQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 67.200α = 90.00
b = 62.300β = 90.50
c = 95.300γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-07
    Type: Initial release
  • Version 1.1: 2012-08-22
    Type: Database references, Other, Structure summary, Version format compliance