1K2O

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 
  • R-Value Work: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: 10.1073/pnas.221297998
  • Primary Citation of 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome P450CAMA, B414Pseudomonas putidaMutation(s): 1 
Gene Names: camCcyp101
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / 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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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