8ET0: Prostaglandin G/H synthase 2

Crystal Complex of murine Cyclooxygenase-2 with alpaca nanobody F9. Determined by X-ray diffraction at 2.15 Å resolution. Released 18 Oct 2023.

Method: X-ray diffraction
Resolution: 2.15 Å
Organisms: Mus musculus, Vicugna pacos
Chains: 4
Atoms: 11,234
Mol. weight: 167.3 kDa
Ligands: IBP, NAG
Released: 18 Oct 2023

Explore 8ET0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ET0 contains 95 α-helices and 89 β-strands across 4 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: 45 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	46-49	4	1
β-strand	55-58	4	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	86-94	9
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
β-strand	265	1	15
α-helix	266-269	4
α-helix	281-283	3
β-strand	285	1	15
α-helix	292-294	3
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	412-417	6
α-helix	419-428	10
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	1
β-strand	512	1	17
β-strand	519	1	17
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, 32 β-strands

Element	Residues	Length	Sheet
β-strand	46-49	4	18
β-strand	55-58	4	18
β-strand	64-65	2	19
β-strand	71-72	2	19
α-helix	74-82	9
α-helix	83-85	3
α-helix	86-94	9
α-helix	97-104	8
α-helix	106-121	16
β-strand	130-131	2	20
β-strand	134	1	20
α-helix	139-143	5
β-strand	147	1	21
β-strand	149-150	2	20
α-helix	153-156	4
β-strand	161	1	22
β-strand	164	1	22
α-helix	171-173	3
α-helix	174-177	4
α-helix	178-182	5
β-strand	183	1	23
β-strand	189	1	24
β-strand	194	1	25
β-strand	195	1	26
α-helix	196-206	11
β-strand	212	1	27
β-strand	220	1	21
β-strand	221	1	27
α-helix	231-234	4
α-helix	238-244	7
β-strand	245	1	28
α-helix	251	1
β-strand	252	1	28
α-helix	253	1
β-strand	255-257	3	29
β-strand	260-262	3	29
β-strand	265	1	30
α-helix	266-269	4
α-helix	281-283	3
β-strand	285	1	30
α-helix	292-294	3
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	20
α-helix	379-384	6
α-helix	388-390	3
β-strand	395-397	3	31
β-strand	400-402	3	31
α-helix	404-407	4
α-helix	412-417	6
α-helix	419-428	10
β-strand	430	1	26
α-helix	431	1
β-strand	432	1	24
α-helix	433	1
β-strand	440	1	23
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	1
β-strand	512	1	32
β-strand	519	1	32
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	25

Chain C: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	33
β-strand	13	1	34
β-strand	20-28	9	33
α-helix	30-32	3
β-strand	33-41	9	35
β-strand	48-54	7	35
β-strand	59-61	3	35
β-strand	66	1	33
β-strand	69-74	6	33
β-strand	79-84	6	33
α-helix	89-91	3
β-strand	93-101	9	35
β-strand	108-110	3	35
β-strand	114-116	3	35
β-strand	117	1	34

Chain D: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	36
β-strand	24-28	5	36
α-helix	30-32	3
β-strand	33-40	8	37
β-strand	48	1	37
β-strand	52-54	3	37
β-strand	59-60	2	37
α-helix	63-65	3
β-strand	72-74	3	36
β-strand	79-81	3	36
α-helix	89-91	3
β-strand	95-101	7	37
β-strand	108-110	3	37

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Prostaglandin G/H synthase 2	A, B	protein	587	Mus musculus	Q05769 (AlphaFold model)
anti-cox-2 alpaca nanobody F9	C, D	protein	140	Vicugna pacos

Sequence of entity 1 (A, B), FASTA

>8ET0_1 Prostaglandin G/H synthase 2 (chains A, B)
ANPCCSNPCQNRGECMSTGFDQYKCDCTRTGFYGENCTTPEFLTRIKLLLKPTPNTVHYI
LTHFKGVWNIVNNIPFLRSLIMKYVLTSRSYLIDSPPTYNVHYGYKSWEAFSNLSYYTRA
LPPVADDCPTPMGVKGNKELPDSKEVLEKVLLRREFIPDPQGSNMMFAFFAQHFTHQFFK
TDHKRGPGFTRGLGHGVDLNHIYGETLDRQHKLRLFKDGKLKYQVIGGEVYPPTVKDTQV
EMIYPPHIPENLQFAVGQEVFGLVPGLMMYATIWLREHNRVCDILKQEHPEWGDEQLFQT
SRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNQQFQYQNRIASEFNTLYHWHPLL
PDTFNIEDQEYSFKQFLYNNSILLEHGLTQFVESFTRQIAGRVAGGRNVPIAVQAVAKAS
IDQSREMKYQSLNEYRKRFSLKPYTSFEELTGEKEMAAELKALYSDIDVMELYPALLVEK
PRPDAIFGETMVELGAPFSLKGLMGNPICSPQYWKPSTFGGEVGFKIINTASIQSLICNN
VKGCPFTSFNVQDPQPTKTATINASASHSRLDDINPTVLIKRRSTEL

Sequence of entity 2 (C, D), FASTA

>8ET0_2 anti-cox-2 alpaca nanobody F9 (chains C, D)
AQVQLQESGGGLVQPGGSLRLSCAASGSIFSIREWGWYRQAPGKQRELVATITSGGTTNY
ADSVRGRFTISRDNAKDTVYLQMNSLTPEDTAVYYCNAESDGWYGLSYWGQGTQVTVGPG
GQHHHHHHGAYPYDVPDYAS

Ligands and cofactors

ID	Name	Formula	Copies
IBP	Ibuprofen	C13 H18 O2	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

Crystal complex of murine cycloxygenase-2 with alpaca nanobody F9. Xu, S., Uddin, M.J. To be published.

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

3NT1 1.73 Å, High resolution structure of naproxen:COX-2 complex.
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…
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

Browse structure collections

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