3FG4

Crystal structure of Delta413-417:GS I805A LOX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

The 1.85 A structure of an 8R-lipoxygenase suggests a general model for lipoxygenase product specificity.

Neau, D.B.Gilbert, N.C.Bartlett, S.G.Boeglin, W.Brash, A.R.Newcomer, M.E.

(2009) Biochemistry 48: 7906-7915

  • DOI: https://doi.org/10.1021/bi900084m
  • Primary Citation of Related Structures:  
    3FG1, 3FG3, 3FG4

  • PubMed Abstract: 

    Lipoxygenases (LOX) play pivotal roles in the biosynthesis of leukotrienes and other biologically active eicosanoids derived from arachidonic acid. A mechanistic understanding of substrate recognition, when lipoxygenases that recognize the same substrate generate different products, can be used to help guide the design of enzyme-specific inhibitors. We report here the 1.85 A resolution structure of an 8R-lipoxygenase from Plexaura homomalla, an enzyme with a sequence approximately 40% identical to that of human 5-LOX. The structure reveals a U-shaped channel, defined by invariant amino acids, that would allow substrate access to the catalytic iron. We demonstrate that mutations within the channel significantly impact enzyme activity and propose a novel model for substrate binding potentially applicable to other members of this enzyme family.


  • Organizational Affiliation

    Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Allene oxide synthase-lipoxygenase protein
A, B, C, D
696Plexaura homomallaMutation(s): 3 
EC: 1.13.11.40
Membrane Entity: Yes 
UniProt
Find proteins for O16025 (Plexaura homomalla)
Explore O16025 
Go to UniProtKB:  O16025
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO16025
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACD
Query on ACD

Download Ideal Coordinates CCD File 
BA [auth B],
DB [auth D],
H [auth A],
NA [auth C]
ARACHIDONIC ACID
C20 H32 O2
YZXBAPSDXZZRGB-DOFZRALJSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
GA [auth B]
HA [auth B]
IA [auth B]
IB [auth D]
JB [auth D]
GA [auth B],
HA [auth B],
IA [auth B],
IB [auth D],
JB [auth D],
KB [auth D],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
UA [auth C],
V [auth A],
VA [auth C],
WA [auth C],
XA [auth C],
Y [auth A],
YA [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY
Query on ACY

Download Ideal Coordinates CCD File 
CA [auth B]
DA [auth B]
EA [auth B]
EB [auth D]
FA [auth B]
CA [auth B],
DA [auth B],
EA [auth B],
EB [auth D],
FA [auth B],
FB [auth D],
GB [auth D],
HB [auth D],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
OA [auth C],
PA [auth C],
QA [auth C],
RA [auth C],
SA [auth C],
TA [auth C]
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
FE2
Query on FE2

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BB [auth D],
E [auth A],
KA [auth C],
Z [auth B]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth C]
CB [auth D]
F [auth A]
G [auth A]
AA [auth B],
AB [auth C],
CB [auth D],
F [auth A],
G [auth A],
LA [auth C],
MA [auth C],
X [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
JA [auth B],
LB [auth D],
W [auth A],
ZA [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.361α = 90
b = 170.382β = 95.51
c = 104.9γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-09-06
    Changes: Data collection, Refinement description