8ET0 | pdb_00008et0

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.214 (Depositor), 0.215 (DCC)
R-Value Work:
0.181 (Depositor), 0.186 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal complex of murine cycloxygenase-2 with alpaca nanobody F9

Xu, S., Uddin, M.J.

To be published.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q05769
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B	Go to GlyGen: Q05769-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	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		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B]
IBP Query on IBP Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B]	I [auth A], L [auth B]	IBUPROFEN C₁₃ H₁₈ O₂ HEFNNWSXXWATRW-JTQLQIEISA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Interactions & Density Focus chain I [auth A] Focus chain L [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
IBP	BindingDB: 8ET0	Ki: min: 7200, max: 1.00e+4 (nM) from 4 assay(s)
IBP	BindingDB: 8ET0	IC50: min: 100, max: 3.70e+5 (nM) from 25 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.214 (Depositor), 0.215 (DCC)
R-Value Work: 0.181 (Depositor), 0.186 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-10-18

Deposition Author(s):

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