1O76 | pdb_00001o76

CYANIDE COMPLEX OF P450CAM FROM PSEUDOMONAS PUTIDA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.236 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Crystal Structures of Cyanide Complexes of P450Cam and the Oxygenase Domain of Inducible Nitric Oxide Synthase-Structural Models of the Short-Lived Oxygen Complexes

Fedorov, R.Ghosh, D.Schlichting, I.

(2003) Arch Biochem Biophys 409: 25

  • DOI: https://doi.org/10.1016/s0003-9861(02)00555-6
  • Primary Citation Related Structures: 
    1N2N, 1O76

  • PubMed Abstract: 

    The crystal structure of the ternary cyanide complex of P450cam and camphor was determined to 1.8A resolution and found to be identical with the structure of the active oxygen complex [I. Schlichting et al., 2000, Science 287, 1615]. Notably, cyanide binds in a bent mode and induces the active conformation that is characterized by the presence of two water molecules and a flip of the carbonyl of the conserved Asp251. The structure of the ternary complex of cyanide, L-arginine, and the oxygenase domain of inducible nitric oxide synthase was determined to 2.4A resolution. Cyanide binds essentially linearly, interacts with L-Arg, and induces the binding of a water molecule at the active site. This water is positioned by backbone interactions, located 2.8A from the nitrogen atom of cyanide, and could provide a proton required for O-O bond scission in the hydroxylation reaction of nitric oxide synthase.


  • Organizational Affiliation
    • Abt. Biophysikalische Chemie, Max Planck Institut für Molekulare Physiologie, Otto Hahn Strasse 11, 44227 Dortmund, Germany.

Macromolecule Content 

  • Total Structure Weight: 95 kDa 
  • Atom Count: 7,480 
  • Modeled Residue Count: 809 
  • Deposited Residue Count: 828 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CYTOCHROME P450-CAM
A, B
414Pseudomonas putidaMutation(s): 0 
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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



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

Query on CAM



Download:Ideal Coordinates CCD File
E [auth A],
K [auth B]
CAMPHOR
C10 H16 O
DSSYKIVIOFKYAU-XCBNKYQSSA-N
TRS

Query on TRS



Download:Ideal Coordinates CCD File
F [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
K

Query on K



Download:Ideal Coordinates CCD File
G [auth B],
J [auth B],
L [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CYN

Query on CYN



Download:Ideal Coordinates CCD File
D [auth A],
I [auth B]
CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.236 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67α = 90
b = 61.8β = 90.4
c = 94.6γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-04-03
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other