1CQE

PROSTAGLANDIN H2 SYNTHASE-1 COMPLEX WITH FLURBIPROFEN

PDB DOI: https://doi.org/10.2210/pdb1CQE/pdb

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

Deposited: 1999-06-15 Released: 1999-06-30
Deposition Author(s): Picot, D., Loll, P.J., Mulichak, A.M., Garavito, R.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.226
R-Value Work: 0.186
R-Value Observed: 0.186

wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

The X-ray crystal structure of the membrane protein prostaglandin H2 synthase-1.

Picot, D., Loll, P.J., Garavito, R.M.

(1994) Nature 367: 243-249

PubMed: 8121489 Search on PubMed
DOI: https://doi.org/10.1038/367243a0
Primary Citation of Related Structures:
1CQE, 1PRH

PubMed Abstract:
The three-dimensional structure of prostaglandin H2 synthase-1, an integral membrane protein, has been determined at 3.5 A resolution by X-ray crystallography. This bifunctional enzyme comprises three independent folding units: an epidermal growth factor domain, a membrane-binding motif and an enzymatic domain. Two adjacent but spatially distinct active sites were found for its haem-dependent peroxidase and cyclooxygenase activities. The cyclooxygenase active site is created by a long, hydrophobic channel that is the site of non-steroidal anti-inflammatory drug binding. The conformation of the membrane-binding motif strongly suggests that the enzyme integrates into only one leaflet of the lipid bilayer and is thus a monotopic membrane protein.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, University of Chicago, Illinois 60637.

Macromolecule Content

Total Structure Weight: 138.92 kDa
Atom Count: 9,413
Modelled Residue Count: 1,105
Deposited Residue Count: 1,160
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (PROSTAGLANDIN H2 SYNTHASE-1)	A, B	580	Ovis aries	Mutation(s): 0 EC: 1.14.99.1
UniProt
Find proteins for P05979 (Ovis aries) Explore P05979 Go to UniProtKB: P05979
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05979
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain P [auth B] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B] mmCIF format, chain L [auth A] mmCIF format, chain P [auth B]	L [auth A], P [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain L [auth A] Focus chain P [auth B]
BOG Query on BOG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain N [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B]	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		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B]
FLP Query on FLP Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain Q [auth B] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain M [auth A] mmCIF format, chain Q [auth B]	M [auth A], Q [auth B]	FLURBIPROFEN C₁₅ H₁₃ F O₂ SYTBZMRGLBWNTM-JTQLQIEISA-N		Interactions Focus chain M [auth A] Focus chain Q [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
FLP	BindingDB: 1CQE	Ki: min: 75, max: 1000 (nM) from 3 assay(s)
FLP	BindingDB: 1CQE	IC50: min: 10, max: 2000 (nM) from 9 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.226
R-Value Work: 0.186
R-Value Observed: 0.186
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.4	α = 90
b = 210.3	β = 90
c = 233.1	γ = 90

Software Package:

Software Name	Purpose
MADNESS	data collection
PROCOR	data scaling
CCP4	data reduction
MLPHARE	phasing
CCP4	model building
X-PLOR	refinement
MADNESS	data reduction
PROCOR	data reduction
CCP4	data scaling
CCP4	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 1999-06-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1999-06-30
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2017-10-04
Changes: Advisory, Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-12-27
Changes: Data collection, Database references, Structure summary
Version 2.2: 2024-10-16
Changes: Structure summary