1DIY

CRYSTAL STRUCTURE OF ARACHIDONIC ACID BOUND IN THE CYCLOOXYGENASE ACTIVE SITE OF PGHS-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The productive conformation of arachidonic acid bound to prostaglandin synthase.

Malkowski, M.G.Ginell, S.L.Smith, W.L.Garavito, R.M.

(2000) Science 289: 1933-1937


  • PubMed Abstract: 
  • Prostaglandin H synthase-1 and -2 (PGHS-1 and -2) catalyze the committed step in prostaglandin synthesis and are targets for nonsteroidal anti-inflammatory drugs (NSAIDs) like aspirin. We have determined the structure of PGHS-1 at 3 angstrom resoluti ...

    Prostaglandin H synthase-1 and -2 (PGHS-1 and -2) catalyze the committed step in prostaglandin synthesis and are targets for nonsteroidal anti-inflammatory drugs (NSAIDs) like aspirin. We have determined the structure of PGHS-1 at 3 angstrom resolution with arachidonic acid (AA) bound in a chemically productive conformation. The fatty acid adopts an extended L-shaped conformation that positions the 13proS hydrogen of AA for abstraction by tyrosine-385, the likely radical donor. A space also exists for oxygen addition on the antarafacial surface of the carbon in the 11-position (C-11). While this conformation allows endoperoxide formation between C-11 and C-9, it also implies that a subsequent conformational rearrangement must occur to allow formation of the C-8/C-12 bond and to position C-15 for attack by a second molecule of oxygen.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-1319, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROSTAGLANDIN H2 SYNTHASE-1
A
553Ovis ariesMutation(s): 0 
Gene Names: PTGS1 (COX1)
EC: 1.14.99.1
Find proteins for P05979 (Ovis aries)
Go to Gene View: PTGS1
Go to UniProtKB:  P05979
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACD
Query on ACD

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A
ARACHIDONIC ACID
C20 H32 O2
YZXBAPSDXZZRGB-DOFZRALJSA-N
 Ligand Interaction
MAN
Query on MAN

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A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
COH
Query on COH

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A
PROTOPORPHYRIN IX CONTAINING CO
C34 H32 Co N4 O4
AQTFKGDWFRRIHR-CTESUSPADG
 Ligand Interaction
BMA
Query on BMA

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A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NDG
Query on NDG

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A
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BOG
Query on BOG

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A
B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.215 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 182.100α = 90.00
b = 182.100β = 90.00
c = 103.640γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSphasing
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-09-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2018-05-30
    Type: Advisory, Data collection, Derived calculations