3KK6

Crystal Structure of Cyclooxygenase-1 in complex with celecoxib

PDB DOI: https://doi.org/10.2210/pdb3KK6/pdb

Classification: OXIDOREDUCTASE
Organism(s): Ovis aries
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2009-11-04 Released: 2009-12-15
Deposition Author(s): Sidhu, R.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.242
R-Value Work: 0.207
R-Value Observed: 0.208

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: 133.74 kDa
Atom Count: 9,372
Modelled Residue Count: 1,106
Deposited Residue Count: 1,106
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 G/H synthase 1	A, B	553	Ovis aries	Mutation(s): 0 Gene Names: COX1, PTGS1 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
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	5		N/A	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G19294PB GlyCosmos: G19294PB GlyGen: G19294PB

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

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	4		N/A	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G26644CA GlyCosmos: G26644CA GlyGen: G26644CA

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 H [auth A] SDF format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B]	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] Interactions & Density Focus chain H [auth A] Focus chain M [auth B]
CEL Query on CEL 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]	4-[5-(4-METHYLPHENYL)-3-(TRIFLUOROMETHYL)-1H-PYRAZOL-1-YL]BENZENESULFONAMIDE C₁₇ H₁₄ F₃ N₃ O₂ S RZEKVGVHFLEQIL-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain N [auth B] Interactions & Density Focus chain I [auth A] Focus chain N [auth B]
BOG Query on BOG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B]	J [auth A], K [auth A], O [auth B], P [auth B]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B]
FLC Query on FLC Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A]	L [auth A]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
CEL	BindingDB: 3KK6	Ki: min: 52, max: 6700 (nM) from 3 assay(s)
CEL	BindingDB: 3KK6	IC50: min: 0.7, max: 7000 (nM) from 39 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.242
R-Value Work: 0.207
R-Value Observed: 0.208
Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.035	α = 90
b = 181.035	β = 90
c = 102.698	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-12-15

Deposition Author(s):

Sidhu, R.S.

Revision History (Full details and data files)

Version 1.0: 2009-12-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2013-03-13
Changes: Refinement description
Version 1.3: 2017-11-01
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: 2023-09-06
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary