3NT1: Naproxen:COX-2 complex

High resolution structure of naproxen:COX-2 complex. Determined by X-ray diffraction at 1.73 Å resolution. Released 1 Sept 2010.

Method: X-ray diffraction
Resolution: 1.73 Å
Organism: Mus musculus
Chains: 2
Atoms: 10,338
Mol. weight: 139.33 kDa
Ligands: NPS, HEM, BOG, NAG
Released: 1 Sept 2010

Explore 3NT1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3NT1 contains 89 α-helices and 62 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 44 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	46-51	6	1
β-strand	54-58	5	1
β-strand	64-65	2	2
β-strand	71-72	2	2
α-helix	74-82	9
α-helix	83-85	3
α-helix	86-93	8
α-helix	97-104	8
α-helix	106-121	16
β-strand	130	1	3
β-strand	131	1	4
β-strand	134	1	4
α-helix	139-143	5
β-strand	147	1	5
β-strand	149	1	6
β-strand	150	1	3
α-helix	153-156	4
β-strand	161	1	7
β-strand	164	1	7
α-helix	171-173	3
α-helix	174-177	4
α-helix	178-182	5
β-strand	183	1	8
β-strand	189	1	9
β-strand	194	1	10
β-strand	195	1	11
α-helix	196-206	11
β-strand	212	1	12
β-strand	220	1	5
β-strand	221	1	12
α-helix	231-234	4
α-helix	238-244	7
β-strand	245	1	13
α-helix	251	1
β-strand	252	1	13
α-helix	253	1
β-strand	255-257	3	14
β-strand	260-262	3	14
α-helix	263-264	2
β-strand	265	1	15
α-helix	266-269	4
α-helix	281-283	3
β-strand	285	1	15
α-helix	296-319	24
α-helix	325-343	19
α-helix	344-349	6
α-helix	350-353	4
α-helix	363-366	4
β-strand	378	1	6
α-helix	379-384	6
α-helix	388-390	3
β-strand	395-397	3	16
β-strand	400-402	3	16
α-helix	404-407	4
α-helix	412-428	17
β-strand	430	1	11
α-helix	431	1
β-strand	432	1	9
α-helix	433	1
β-strand	440	1	8
α-helix	442-444	3
α-helix	445-457	13
α-helix	460-462	3
α-helix	463-469	7
α-helix	473-475	3
α-helix	478-482	5
α-helix	486-495	10
α-helix	498-500	3
α-helix	503-509	7
α-helix	511-512	2
α-helix	520-535	16
α-helix	538-540	3
α-helix	547-550	4
α-helix	553-560	8
α-helix	564-571	8
β-strand	581	1	10

Chain B: 45 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	45	1
β-strand	46-49	4	17
β-strand	55-58	4	17
β-strand	64-65	2	18
β-strand	71-72	2	18
α-helix	74-82	9
α-helix	83-85	3
α-helix	86-93	8
α-helix	97-104	8
α-helix	106-121	16
β-strand	130-131	2	19
β-strand	134	1	19
α-helix	139-143	5
β-strand	147	1	20
α-helix	148	1
β-strand	149-150	2	19
α-helix	153-156	4
β-strand	161	1	21
β-strand	164	1	21
α-helix	171-173	3
α-helix	174-177	4
α-helix	178-182	5
β-strand	183	1	22
β-strand	189	1	23
β-strand	194	1	24
β-strand	195	1	25
α-helix	196-206	11
β-strand	212	1	26
β-strand	220	1	20
β-strand	221	1	26
α-helix	231-234	4
α-helix	238-244	7
β-strand	245	1	27
α-helix	251	1
β-strand	252	1	27
α-helix	253	1
β-strand	255-257	3	28
β-strand	260-262	3	28
β-strand	265	1	29
α-helix	266-269	4
α-helix	281-283	3
β-strand	285	1	29
α-helix	296-319	24
α-helix	325-343	19
α-helix	344-349	6
α-helix	350-353	4
α-helix	363-366	4
β-strand	378	1	19
α-helix	379-384	6
α-helix	388-390	3
β-strand	395-397	3	30
β-strand	400-402	3	30
α-helix	404-407	4
α-helix	412-428	17
β-strand	430	1	25
α-helix	431	1
β-strand	432	1	23
α-helix	433	1
β-strand	440	1	22
α-helix	442-444	3
α-helix	445-457	13
α-helix	460-462	3
α-helix	463-469	7
α-helix	472-475	4
α-helix	478-482	5
α-helix	486-495	10
α-helix	498-500	3
α-helix	503-509	7
α-helix	511-512	2
α-helix	520-535	16
α-helix	538-540	3
α-helix	547-550	4
α-helix	553-560	8
α-helix	564-571	8
β-strand	581	1	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Prostaglandin-endoperoxide synthase 2	A, B	protein	587	Mus musculus	Q05769 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3NT1_1 Prostaglandin-endoperoxide synthase 2 (chains A, B)
ANPCCSNPCQNRGECMSTGFDQYKCDCTRTGFYGENCTTPEFLTRIKLLLKPTPNTVHYI
LTHFKGVWNIVNNIPFLRSLIMKYVLTSRSYLIDSPPTYNVHYGYKSWEAFSNLSYYTRA
LPPVADDCPTPMGVKGNKELPDSKEVLEKVLLRREFIPDPQGSNMMFAFFAQHFTHQFFK
TDHKRGPGFTRGLGHGVDLNHIYGETLDRQHKLRLFKDGKLKYQVIGGEVYPPTVKDTQV
EMIYPPHIPENLQFAVGQEVFGLVPGLMMYATIWLREHNRVCDILKQEHPEWGDEQLFQT
SRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNQQFQYQNRIASEFNTLYHWHPLL
PDTFNIEDQEYSFKQFLYNNSILLEHGLTQFVESFTRQIAGRVAGGRNVPIAVQAVAKAS
IDQSREMKYQSLNEYRKRFSLKPYTSFEELTGEKEMAAELKALYSDIDVMELYPALLVEK
PRPDAIFGETMVELGAPFSLKGLMGNPICSPQYWKPSTFGGEVGFKIINTASIQSLICNN
VKGCPFTSFNVQDPQPTKTATINASASHSRLDDINPTVLIKRRSTEL

Ligands and cofactors

ID	Name	Formula	Copies
NPS	(2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid	C14 H14 O3	2
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	2
BOG	octyl beta-D-glucopyranoside	C14 H28 O6	4
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Water and common crystallization additives (CL) are not listed.

Primary citation

Molecular basis for cyclooxygenase inhibition by the non-steroidal anti-inflammatory drug naproxen. Duggan, K.C., Walters, M.J., Musee, J. et al. J Biol Chem (2010) 285:34950-34959. DOI 10.1074/jbc.M110.162982 · PubMed

Other PDB entries of the same protein (UniProt Q05769 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4PH9 1.81 Å, The structure of Ibuprofen bound to cyclooxygenase-2
5FDQ 1.9 Å, Murine COX-2 S530T mutant
4M10 2.01 Å, Crystal Structure of Murine Cyclooxygenase-2 Complex with Isoxicam
3HS5 2.1 Å, X-ray crystal structure of arachidonic acid bound to the cyclooxygenase channel of…
3QH0 2.1 Å, X-ray crystal structure of palmitic acid bound to the cyclooxygenase channel of…
4E1G 2.1 Å, X-ray crystal structure of alpha-linolenic acid bound to the cyclooxygenase channel of…
4OTJ 2.11 Å, The complex of murine cyclooxygenase-2 with a conjugate of indomefathin and…
3TZI 2.15 Å, X-ray crystal structure of arachidonic acid bound in the cyclooxygenase channel of G533V…
8ET0 2.15 Å, Crystal Complex of murine Cyclooxygenase-2 with alpaca nanobody F9
4RUT 2.16 Å, crystal structure of murine cyclooxygenase-2 with 13-methyl-arachidonic Acid
3NTG 2.19 Å, Crystal structure of COX-2 with selective compound 23d-(R)
3LN0 2.2 Å, Structure of compound 5c-S bound at the active site of COX-2

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