1K2O | pdb_00001k2o

Cytochrome P450Cam with Bound BIS(2,2'-BIPYRIDINE)-(5-METHYL-2-2'-BIPYRIDINE)-C2-ADAMANTANE RUTHENIUM (II)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.226 (Depositor) 
  • R-Value Work: 
    0.210 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 1K2O

This is version 1.4 of the entry. See complete history

Literature

Probing the open state of cytochrome P450cam with ruthenium-linker substrates.

Dunn, A.R.Dmochowski, I.J.Bilwes, A.M.Gray, H.B.Crane, B.R.

(2001) Proc Natl Acad Sci U S A 98: 12420-12425

  • DOI: https://doi.org/10.1073/pnas.221297998
  • Primary Citation Related Structures: 
    1K2O

  • PubMed Abstract: 

    Cytochromes P450 play key roles in drug metabolism and disease by oxidizing a wide variety of natural and xenobiotic compounds. High-resolution crystal structures of P450cam bound to ruthenium sensitizer-linked substrates reveal an open conformation of the enzyme that allows substrates to access the active center via a 22-A deep channel. Interactions of alkyl and fluorinated biphenyl linkers with the channel demonstrate the importance of exploiting protein dynamics for specific inhibitor design. Large changes in peripheral enzyme structure (F and G helices) couple to conformational changes in active center residues (I helix) implicated in proton pumping and dioxygen activation. Common conformational states among P450cam and homologous enzymes indicate that static and dynamic variability in the F/G helix region allows the 54 human P450s to oxidize thousands of substrates.


  • Organizational Affiliation
    • The Beckman Institute, MC 139-74, California Institute of Technology, Pasadena, CA 91125, USA.

Macromolecule Content 

  • Total Structure Weight: 99.33 kDa 
  • Atom Count: 7,649 
  • Modeled Residue Count: 812 
  • Deposited Residue Count: 828 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome P450CAM
A, B
414Pseudomonas putidaMutation(s): 1 
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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RFB

Query on RFB



Download:Ideal Coordinates CCD File
G [auth A],
M [auth B]
LAMBDA-BIS(2,2'-BIPYRIDINE)-(5-METHYL-2-2'-BIPYRIDINE)-C2-ADAMANTANE RUTHENIUM (II)
C54 H75 F8 N7 Ru
QXSHRHKMCRAIGC-DMCKNCFYSA-N
RFA

Query on RFA



Download:Ideal Coordinates CCD File
F [auth A],
L [auth B]
DELTA-BIS(2,2'-BIPYRIDINE)-(5-METHYL-2-2'-BIPYRIDINE)-C2-ADAMANTANE RUTHENIUM (II)
C54 H75 F8 N7 Ru
QXSHRHKMCRAIGC-QMGQRXOWSA-N
HEM

Query on HEM



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

Query on CAC



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
H [auth B],
I [auth B],
J [auth B]
CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.226 (Depositor) 
  • R-Value Work:  0.210 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.87α = 71.16
b = 67.05β = 65.2
c = 72.52γ = 62.31
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-10-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-16
    Changes: Data collection, Refinement description