2AYL

2.0 Angstrom Crystal Structure of Manganese Protoporphyrin IX-reconstituted Ovine Prostaglandin H2 Synthase-1 Complexed With Flurbiprofen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.218 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

2.0 angstroms structure of prostaglandin H2 synthase-1 reconstituted with a manganese porphyrin cofactor.

Gupta, K.Selinsky, B.S.Loll, P.J.

(2006) Acta Crystallogr D Biol Crystallogr 62: 151-156

  • DOI: 10.1107/S0907444905036309
  • Primary Citation of Related Structures:  
    2AYL

  • PubMed Abstract: 
  • Prostaglandin H2 synthase (EC 1.14.99.1) is a clinically important drug target that catalyzes two key steps in the biosynthesis of the eicosanoid hormones. The enzyme contains spatially distinct cyclooxygenase and peroxidase active sites, both of which require a heme cofactor ...

    Prostaglandin H2 synthase (EC 1.14.99.1) is a clinically important drug target that catalyzes two key steps in the biosynthesis of the eicosanoid hormones. The enzyme contains spatially distinct cyclooxygenase and peroxidase active sites, both of which require a heme cofactor. Substitution of ferric heme by Mn(III) protoporphyrin IX greatly diminishes the peroxidase activity, but has little effect on the cyclooxygenase activity. Here, the 2.0 angstroms resolution crystal structure of the Mn(III) form of ovine prostaglandin H2 synthase-1 is described (R = 21.8%, R(free) = 23.7%). Substitution of Mn(III) for Fe(III) causes no structural perturbations in the protein. However, the out-of-plane displacement of the manganese ion with respect to the porphyrin is greater than that of the iron by approximately 0.2 angstroms. This perturbation may help to explain the altered catalytic properties of the manganese enzyme.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Prostaglandin G/H synthase 1A, B553Ovis ariesMutation(s): 0 
Gene Names: PTGS1COX1
EC: 1.14.99.1
UniProt
Find proteins for P05979 (Ovis aries)
Explore P05979 
Go to UniProtKB:  P05979
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC, F2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-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-glucopyranoseD, G5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G27747YT
GlyCosmos:  G27747YT
GlyGen:  G27747YT
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D 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-glucopyranoseE, H4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G04854NQ
GlyCosmos:  G04854NQ
GlyGen:  G04854NQ
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MNH
Query on MNH

Download Ideal Coordinates CCD File 
N [auth A], V [auth B]MANGANESE PROTOPORPHYRIN IX
C34 H32 Mn N4 O4
UIBYYPDLEONCGQ-RGGAHWMASA-L
 Ligand Interaction
BOG
Query on BOG

Download Ideal Coordinates CCD File 
I [auth A], J [auth A], K [auth A], L [auth A], R [auth B], S [auth B], T [auth B]octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
FLP
Query on FLP

Download Ideal Coordinates CCD File 
M [auth A], U [auth B]FLURBIPROFEN
C15 H13 F O2
SYTBZMRGLBWNTM-JTQLQIEISA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
O [auth A], P [auth A], Q [auth A], W [auth B], X [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FLPIC50:  500   nM  BindingDB
FLPIC50:  30   nM  BindingDB
FLPIC50:  150   nM  BindingDB
FLPKi:  75   nM  BindingDB
FLPIC50:  1995   nM  BindingDB
FLPIC50:  2000   nM  BindingDB
FLPKi:  1000   nM  BindingDB
FLPIC50:  10   nM  BindingDB
FLPIC50:  11   nM  BindingDB
FLPIC50:  12   nM  BindingDB
FLPIC50:  170   nM  BindingDB
FLPKi:  410   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.218 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.931α = 90
b = 206.55β = 90
c = 221.553γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
d*TREKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary