1CVU

CRYSTAL STRUCTURE OF ARACHIDONIC ACID BOUND TO THE CYCLOOXYGENASE ACTIVE SITE OF COX-2

• PDB DOI: https://doi.org/10.2210/pdb1CVU/pdb

• Classification: OXIDOREDUCTASE/peptide
• Organism(s): Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 1999-08-24 Released: 2000-05-16 
• Deposition Author(s): Kiefer, J.R., Pawlitz, J.L., Moreland, K.T., Stegeman, R.A., Gierse, J.K., Stevens, A.M., Goodwin, D.C., Rowlinson, S.W., Marnett, L.J., Stallings, W.C., Kurumbail, R.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.235 
• R-Value Work: 0.204 

Literature

Structural insights into the stereochemistry of the cyclooxygenase reaction.

Kiefer, J.R., Pawlitz, J.L., Moreland, K.T., Stegeman, R.A., Hood, W.F., Gierse, J.K., Stevens, A.M., Goodwin, D.C., Rowlinson, S.W., Marnett, L.J., Stallings, W.C., Kurumbail, R.G.

(2000) Nature 405: 97-101

• PubMed: 10811226 
• DOI: https://doi.org/10.1038/35011103
• Primary Citation of Related Structures:  
  1CVU, 1DDX


• PubMed Abstract: 
  

  Cyclooxygenases are bifunctional enzymes that catalyse the first committed step in the synthesis of prostaglandins, thromboxanes and other eicosanoids. The two known cyclooxygenases isoforms share a high degree of amino-acid sequence similarity, structural topology and an identical catalytic mechanism. Cyclooxygenase enzymes catalyse two sequential reactions in spatially distinct, but mechanistically coupled active sites. The initial cyclooxygenase reaction converts arachidonic acid (which is achiral) to prostaglandin G2 (which has five chiral centres). The subsequent peroxidase reaction reduces prostaglandin G2 to prostaglandin H2. Here we report the co-crystal structures of murine apo-cyclooxygenase-2 in complex with arachidonic acid and prostaglandin. These structures suggest the molecular basis for the stereospecificity of prostaglandin G2 synthesis.

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Organizational Affiliation: 

Searle Discovery Research, Monsanto Company, St Louis, Missouri 63198, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 132.6 kDa 
• Atom Count: 10,100 
• Modelled Residue Count: 1,113 
• Deposited Residue Count: 1,113 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROSTAGLANDIN H2 SYNTHASE-2	A, B	552	Mus musculus	Mutation(s): 2  EC: 1.14.99.1
UniProt
Find proteins for Q05769 (Mus musculus) Explore Q05769  Go to UniProtKB:  Q05769
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: Q05769-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (9-MER)	C [auth F]	9	N/A	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth C], F [auth E]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth D], G	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G04854NQ GlyCosmos:  G04854NQ GlyGen:  G04854NQ

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACD	L [auth A], P [auth B]	ARACHIDONIC ACID C20 H32 O2 YZXBAPSDXZZRGB-DOFZRALJSA-N
BOG	I [auth A], J [auth A], K [auth A], N [auth B], O [auth B]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
NAG	H [auth A], M [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ACD	BindingDB:  1CVU	Kd: 8070 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.235 
• R-Value Work: 0.204 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.036	α = 90
b = 133.96	β = 90
c = 124.834	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-05-16 
Deposition Author(s): Kiefer, J.R., Pawlitz, J.L., Moreland, K.T., Stegeman, R.A., Gierse, J.K., Stevens, A.M., Goodwin, D.C., Rowlinson, S.W., Marnett, L.J., Stallings, W.C., Kurumbail, R.G.

Revision History  

• Version 1.0: 2000-05-16
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2021-11-03
  Changes: Database references, Structure summary
• Version 2.2: 2024-11-20
  Changes: Data collection, Structure summary