1PTH

The Structural Basis of Aspirin Activity Inferred from the Crystal Structure of Inactivated Prostaglandin H2 Synthase

PDB DOI: https://doi.org/10.2210/pdb1PTH/pdb

Classification: OXIDOREDUCTASE
Organism(s): Ovis aries
Mutation(s): No
Membrane Protein: Yes mpstruc

Deposited: 1995-04-11 Released: 1996-04-11
Deposition Author(s): Loll, P.J., Picot, D., Garavito, R.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.227
R-Value Work: 0.186
R-Value Observed: 0.186

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 136.4 kDa
Atom Count: 9,221
Modelled Residue Count: 1,102
Deposited Residue Count: 1,152
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROSTAGLANDIN H2 SYNTHASE-1	A, B	576	Ovis aries	Mutation(s): 0 EC: 1.14.99.1 Membrane Entity: Yes
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
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	2		N-Glycosylation	Interactions Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A]	H [auth A], M [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain H [auth A] Focus chain M [auth B]
BOG Query on BOG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B]	G [auth A], L [auth B]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B]	E [auth A], F [auth A], J [auth B], K [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B]
SAL Query on SAL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain N [auth B] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B]	I [auth A], N [auth B]	2-HYDROXYBENZOIC ACID C₇ H₆ O₃ YGSDEFSMJLZEOE-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain N [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
0AH Query on 0AH	A, B	L-PEPTIDE LINKING	C₅ H₈ Br N O₄		SER

Binding Affinity Annotations
ID	Source	Binding Affinity
SAL	BindingDB: 1PTH	Ki: 1.00e+4 (nM) from 1 assay(s)
SAL	BindingDB: 1PTH	IC50: min: 4.00e+4, max: 5.00e+5 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.227
R-Value Work: 0.186
R-Value Observed: 0.186
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.57	α = 90
b = 209.8	β = 90
c = 235	γ = 90

Software Package:

Software Name	Purpose
MADNES	data collection
X-PLOR	model building
X-PLOR	refinement
MADNES	data reduction
X-PLOR	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 1996-04-11

Deposition Author(s):

Loll, P.J.

Picot, D.

Garavito, R.M.

Revision History (Full details and data files)

Version 1.0: 1996-04-11
Type: Initial release
Version 1.1: 2008-03-03
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: Atomic model, Data collection, Derived calculations, Other, Structure summary