8ET0

Crystal Complex of murine Cyclooxygenase-2 with alpaca nanobody F9

• PDB DOI: https://doi.org/10.2210/pdb8ET0/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Mus musculus, Vicugna pacos
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 


• Deposited: 2022-10-15 Released: 2023-10-18 
• Deposition Author(s): Xu, S., Banerjee, S., Uddin, M.J., Goodman, M.C., Marnett, L.J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.214 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Crystal complex of murine cycloxygenase-2 with alpaca nanobody F9

Xu, S., Uddin, M.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 167.3 kDa 
• Atom Count: 11,234 
• Modelled Residue Count: 1,314 
• Deposited Residue Count: 1,454 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prostaglandin G/H synthase 2	A, B	587	Mus musculus	Mutation(s): 0  Gene Names: Ptgs2, Cox-2, Cox2, Pghs-b, Tis10 EC: 1.14.99.1
UniProt
Find proteins for Q05769 (Mus musculus) Explore Q05769  Go to UniProtKB:  Q05769
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: Q05769-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-cox-2 alpaca nanobody F9	C, D	140	Vicugna pacos	Mutation(s): 0

Oligosaccharides

Help

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth A], H [auth A], J [auth B], K [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
IBP	I [auth A], L [auth B]	IBUPROFEN C13 H18 O2 HEFNNWSXXWATRW-JTQLQIEISA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
IBP	BindingDB:  8ET0	Ki: min: 7200, max: 1.00e+4 (nM) from 4 assay(s)
		IC50: min: 100, max: 3.70e+5 (nM) from 28 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.214 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.526	α = 90
b = 141.526	β = 90
c = 90.429	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-10-18 
Deposition Author(s): Xu, S., Banerjee, S., Uddin, M.J., Goodman, M.C., Marnett, L.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM15431
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	CA089450

Revision History  

• Version 1.0: 2023-10-18
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Structure summary