Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 136.10 kDa 
• Atom Count: 10336 
• Residue Count: 1106 
• Unique protein chains: 1

1Q4G

2.0 Angstrom Crystal Structure of Ovine Prostaglandin H2 Synthase-1, in complex with alpha-methyl-4-biphenylacetic acid

• DOI: 10.2210/pdb1Q4G/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Ovis aries
• Mutation(s): No 


• Deposited: 2003-08-03 Released: 2004-01-06 
• Deposition Author(s): Gupta, K., Selinksy, B.S., Kaub, C.J., Katz, A.K., Loll, P.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.231 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 

Literature

The 2.0A Resolution Crystal Structure of Prostaglandin H(2) Synthase-1: Structural Insights into an Unusual Peroxidase

Gupta, K., Selinsky, B.S., Kaub, C.J., Katz, A.K., Loll, P.J.

(2004) J Mol Biol 335: 503-518

• PubMed: 14672659 
• DOI: 10.1016/j.jmb.2003.10.073
• Primary Citation of Related Structures:  
  1Q4G


• PubMed Abstract: 
  

Prostaglandin H2 synthase (EC 1.14.99.1) is an integral membrane enzyme containing a cyclooxygenase site, which is the target for the non-steroidal anti-inflammatory drugs, and a spatially distinct peroxidase site. Previous crystallographic studies of this clinically important drug target have been hindered by low resolution. We present here the 2.0 A resolution X-ray crystal structure of ovine prostaglandin H2 synthase-1 in complex with alpha-methyl-4-biphenylacetic acid, a defluorinated analog of the non-steroidal anti-inflammatory drug flurbiprofen. Detergent molecules are seen to bind to the protein's membrane-binding domain, and their positions suggest the depth to which this domain is likely to penetrate into the lipid bilayer. The relation of the enzyme's proximal heme ligand His388 to the heme iron is atypical for a peroxidase; the iron-histidine bond is unusually long and a substantial tilt angle is observed between the heme and imidazole planes. A molecule of glycerol, used as a cryoprotectant during diffraction experiments, is seen to bind in the peroxidase site, offering the first view of any ligand in this active site. Insights gained from glycerol binding may prove useful in the design of a peroxidase-specific ligand.

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Organizational Affiliation: 

Department of Biochemistry, Drexel University College of Medicine, 245 N 15th Street, Mailstop 497, Philadelphia, PA 19102-1192, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prostaglandin G/H synthase 1	A, B	553	Ovis aries	Mutation(s): 0  Gene Names: PTGS1, COX1 EC: 1.14.99.1
Find proteins for P05979 (Ovis aries) Explore P05979  Go to UniProtKB:  P05979

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, F	2		N-Glycosylation

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, G	4		N-Glycosylation

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	5		N-Glycosylation

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H	5		N-Glycosylation

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	A, B	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
BOG	A, B	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
BFL	A, B	2-(1,1'-BIPHENYL-4-YL)PROPANOIC ACID C15 H14 O2 JALUUBQFLPUJMY-NSHDSACASA-N
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
BFL	IC50:  110   nM  BindingDB
BFL	Ki:  130   nM  BindingDB
BFL	IC50:  10   nM  BindingDB
BFL	IC50:  32   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.231 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.147	α = 90
b = 203.859	β = 90
c = 223.599	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-08-03 
• Released Date: 2004-01-06 
Deposition Author(s): Gupta, K., Selinksy, B.S., Kaub, C.J., Katz, A.K., Loll, P.J.

Revision History 

• Version 1.0: 2004-01-06
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2014-11-12
  Changes: Derived calculations
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary