1Q4G

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

PDB DOI: https://doi.org/10.2210/pdb1Q4G/pdb

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

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.

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 136.1 kDa
Atom Count: 10,336
Modelled Residue Count: 1,106
Deposited Residue Count: 1,106
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prostaglandin G/H synthase 1	A, B	553	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

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, F	2		N-Glycosylation	Interactions Focus chain C Focus chain F Interactions & Density Focus chain C Focus chain F
Glycosylation Resources
GlyTouCan: G07375KG GlyCosmos: G07375KG GlyGen: G07375KG

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	Interactions Focus chain D Focus chain G Interactions & Density Focus chain D Focus chain G
Glycosylation Resources
GlyTouCan: G40894EI GlyCosmos: G40894EI GlyGen: G40894EI

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G42831WZ GlyCosmos: G42831WZ GlyGen: G42831WZ

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G07860ZO GlyCosmos: G07860ZO GlyGen: G07860ZO

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 V [auth B] SDF format, chain N [auth A] MOL2 format, chain V [auth B] MOL2 format, chain N [auth A]	N [auth A], V [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain N [auth A] Focus chain V [auth B] Interactions & Density Focus chain N [auth A] Focus chain V [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 L [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B]	I [auth A] J [auth A] K [auth A] L [auth A] Q [auth B] I [auth A], J [auth A], K [auth A], L [auth A], Q [auth B], R [auth B], S [auth B], T [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 L [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
BFL Query on BFL Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain U [auth B] MOL2 format, chain M [auth A] MOL2 format, chain U [auth B]	M [auth A], U [auth B]	2-(1,1'-BIPHENYL-4-YL)PROPANOIC ACID C₁₅ H₁₄ O₂ JALUUBQFLPUJMY-NSHDSACASA-N		Interactions Focus chain M [auth A] Focus chain U [auth B] Interactions & Density Focus chain M [auth A] Focus chain U [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B]	O [auth A], P [auth A], W [auth B], X [auth B], Y [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain P [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain O [auth A] Focus chain P [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
BFL	BindingDB: 1Q4G	Ki: 130 (nM) from 1 assay(s)
BFL	BindingDB: 1Q4G	IC50: min: 10, max: 110 (nM) from 3 assay(s)

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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2004-01-06

Deposition Author(s):

Revision History (Full details and data files)

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
Version 2.1: 2023-08-16
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

1Q4G

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

Glycosylation Resources

Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)