1AKD | pdb_00001akd

CYTOCHROME P450CAM FROM PSEUDOMONAS PUTIDA, COMPLEXED WITH 1S-CAMPHOR

• PDB DOI: https://doi.org/10.2210/pdb1AKD/pdb

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


• Deposited: 1997-05-16 Released: 1997-11-19 
• Deposition Author(s): Schlichting, I., Jung, C., Schulze, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.265 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: other

Literature

Crystal structure of cytochrome P-450cam complexed with the (1S)-camphor enantiomer.

Schlichting, I., Jung, C., Schulze, H.

(1997) FEBS Lett 415: 253-257

• PubMed: 9357977 
• DOI: https://doi.org/10.1016/s0014-5793(97)01135-6
• Primary Citation Related Structures: 
  1AKD


• PubMed Abstract: 
  

  The crystal structure of cytochrome P-450cam complexed with the enantiomer (1S)-camphor has been solved to 1.8 angstroms resolution and compared with the structure of the (1R)-camphor P-450cam complex. The overall protein structure is the same for both enantiomer complexes. However, the orientation of the substrates in the heme pocket differs. In contrast to (1R)-camphor, the (1S)-enantiomer binds in at least two orientations. The major binding mode of (1S)-camphor resembles the one of the (1R)-enantiomer in that there is a hydrogen bond between Tyr-96 and the quinone group of camphor, and the 10-methyl group points towards the I-helix. The binding differs in that C-5 is not at a position suitable for hydroxylation. In the other orientation (1S)-camphor is not hydrogen bonded, but C-5 is located suitably for hydroxylation.

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Organizational Affiliation: 
• Max Planck Institute for Molecular Physiology, Division for Physical Biochemistry, Dortmund, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 47.4 kDa 
• Atom Count: 3,545 
• Modeled Residue Count: 405 
• Deposited Residue Count: 414 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME P450CAM	A	414	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
CAM	D [auth A]	CAMPHOR C10 H16 O DSSYKIVIOFKYAU-XCBNKYQSSA-N
K	B [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.265 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.3	α = 90
b = 66.2	β = 90
c = 106.8	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-11-19 
Deposition Author(s): Schlichting, I., Jung, C., Schulze, H.

Revision History  

• Version 1.0: 1997-11-19
  Type: Initial release
  
• Version 1.1: 2008-03-05
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.4: 2024-04-03
  Changes: Refinement description