1FAG | pdb_00001fag

STRUCTURE OF CYTOCHROME P450


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.353 (Depositor), 0.320 (DCC) 
  • R-Value Work: 
    0.246 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 
    0.246 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

The structure of the cytochrome p450BM-3 haem domain complexed with the fatty acid substrate, palmitoleic acid.

Li, H.Poulos, T.L.

(1997) Nat Struct Biol 4: 140-146

  • DOI: https://doi.org/10.1038/nsb0297-140
  • Primary Citation Related Structures: 
    1FAG

  • PubMed Abstract: 

    The substrate-bound structures of two cytochrome P450s, P450cam and P450eryF, are known. While these structures reveal important features that control substrate specificity, the problem of how conformational changes allow for substrate entry and product release remains unsolved. The structure of the haem domain of the bacterial fatty acid hydroxylase, P450BM-3, previously was solved in the substrate-free form. Unlike the substrate-bound P450cam and P450eryF structures, the substrate access channel is open in substrate-free P450BM-3. Here we present the X-ray structure of P450BM-3 at 2.7 A bound with a fatty acid substrate, palmitoleic acid. A comparison of the substrate-bound and -free forms reveals major conformational differences and provides the first detailed picture of substrate-induced conformational changes in a P450.


  • Organizational Affiliation
    • Department of Molecular Biology and Biochemistry, University of California at Irvine 92697, USA.

Macromolecule Content 

  • Total Structure Weight: 218.67 kDa 
  • Atom Count: 14,924 
  • Modeled Residue Count: 1,820 
  • Deposited Residue Count: 1,884 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CYTOCHROME P450 BM-3
A, B, C, D
471Priestia megateriumMutation(s): 0 
EC: 1.14.14.1 (PDB Primary Data), 1.6.2.4 (UniProt)
UniProt
Find proteins for P14779 (Priestia megaterium (strain ATCC 14581 / DSM 32 / CCUG 1817 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / NRRL B-14308 / VKM B-512 / Ford 19))
Explore P14779 
Go to UniProtKB:  P14779
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14779
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



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

Query on PAM



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B],
J [auth C],
L [auth D]
PALMITOLEIC ACID
C16 H30 O2
SECPZKHBENQXJG-FPLPWBNLSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.353 (Depositor), 0.320 (DCC) 
  • R-Value Work:  0.246 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 0.246 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.2α = 90
b = 165.2β = 90
c = 223.9γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
CCP4data scaling
ROTAVATAdata scaling
TRUNCATEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-02-12
    Type: Initial release
  • Version 1.1: 2008-03-03
    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, Refinement description
  • Version 1.4: 2024-04-03
    Changes: Refinement description