3MDL: 1-arachidonoyl glycerol

X-ray crystal structure of 1-arachidonoyl glycerol bound to the cyclooxygenase channel of cyclooxygenase-2. Determined by X-ray diffraction at 2.2 Å resolution. Released 13 Apr 2011.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Mus musculus
Chains: 2
Atoms: 10,254
Mol. weight: 140.15 kDa
Ligands: 1AG, COH, NAG, BOG
Released: 13 Apr 2011

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

Secondary structure: helices and β-sheets

3MDL contains 87 α-helices and 60 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: 43 helices, 30 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	86-93	8
α-helix	97-105	9
α-helix	106-121	16
β-strand	130-131	2	3
β-strand	134	1	3
α-helix	139-143	5
β-strand	147	1	4
β-strand	149-150	2	3
α-helix	153-156	4
β-strand	161	1	5
β-strand	164	1	5
α-helix	174-177	4
α-helix	178-182	5
β-strand	183	1	6
β-strand	189	1	7
β-strand	194	1	8
β-strand	195	1	9
α-helix	196-206	11
β-strand	212	1	10
β-strand	220	1	4
β-strand	221	1	10
α-helix	231-234	4
α-helix	238-244	7
β-strand	245	1	11
α-helix	251	1
β-strand	252	1	11
α-helix	253	1
β-strand	255-257	3	12
β-strand	260-262	3	12
α-helix	263-264	2
β-strand	265	1	13
α-helix	266-269	4
α-helix	281-283	3
β-strand	285	1	13
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	3
α-helix	379-384	6
α-helix	388-390	3
β-strand	395-397	3	14
β-strand	400-402	3	14
α-helix	404-407	4
α-helix	411-428	18
β-strand	430	1	9
α-helix	431	1
β-strand	432	1	7
α-helix	433	1
β-strand	440	1	6
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	8

Chain B: 44 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	45	1
β-strand	46-49	4	15
β-strand	55-58	4	15
β-strand	64-65	2	16
β-strand	71-72	2	16
α-helix	74-82	9
α-helix	83-85	3
α-helix	86-94	9
α-helix	97-103	7
α-helix	106-121	16
β-strand	130-131	2	17
β-strand	134	1	17
α-helix	139-143	5
β-strand	147	1	18
β-strand	149-150	2	17
α-helix	153-156	4
β-strand	161	1	19
β-strand	164	1	19
α-helix	174-177	4
α-helix	178-182	5
β-strand	183	1	20
β-strand	189	1	21
β-strand	194	1	22
β-strand	195	1	23
α-helix	196-206	11
β-strand	212	1	24
β-strand	220	1	18
β-strand	221	1	24
α-helix	231-234	4
α-helix	238-244	7
β-strand	245	1	25
α-helix	251	1
β-strand	252	1	25
α-helix	253	1
β-strand	255-257	3	26
β-strand	260-262	3	26
β-strand	265	1	27
α-helix	266-269	4
α-helix	281-283	3
β-strand	285	1	27
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	17
α-helix	379-384	6
α-helix	388-390	3
β-strand	395-397	3	28
β-strand	400-402	3	28
α-helix	404-407	4
α-helix	412-428	17
β-strand	430	1	23
α-helix	431	1
β-strand	432	1	21
α-helix	433	1
β-strand	440	1	20
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	22

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>3MDL_1 Prostaglandin G/H synthase 2 (chains A, B)
NHHHHHHPCCSNPCQNRGECMSTGFDQYKCDCTRTGFYGENCTTPEFLTRIKLLLKPTPN
TVHYILTHFKGVWNIVNNIPFLRSLIMKYVLTSRSYLIDSPPTYNVHYGYKSWEAFSNLS
YYTRALPPVADDCPTPMGVKGNKELPDSKEVLEKVLLRREFIPDPQGSNMMFAFFAQHFT
HQFFKTDHKRGPGFTRGLGHGVDLNHIYGETLDRQHKLRLFKDGKLKYQVIGGEVYPPTV
KDTQVEMIYPPHIPENLQFAVGQEVFGLVPGLMMYATIWLREHNRVCDILKQEHPEWGDE
QLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNQQFQYQNRIASEFNTLYH
WHPLLPDTFNIEDQEYSFKQFLYNNSILLEHGLTQFVESFTRQIAGRVAGGRNVPIAVQA
VAKASIDQSREMKYQSLNEYRKRFSLKPYTSFEELTGEKEMAAELKALYSDIDVMELYPA
LLVEKPRPDAIFGETMVELGAPFSLKGLMGNPICSPQYWKPSTFGGEVGFKIINTASIQS
LICNNVKGCPFTSFNVQDPQPTKTATIAASASHSRLDDINPTVLIKR

Ligands and cofactors

ID	Name	Formula	Copies
1AG	(2S)-2,3-dihydroxypropyl (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate	C23 H38 O4	2
COH	Protoporphyrin IX containing co	C34 H32 Co N4 O4	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
BOG	octyl beta-D-glucopyranoside	C14 H28 O6	1
AKR	Acrylic acid	C3 H4 O2	5

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

Primary citation

The structural basis of endocannabinoid oxygenation by cyclooxygenase-2. Vecchio, A.J., Malkowski, M.G. J Biol Chem (2011) 286:20736-20745. DOI 10.1074/jbc.M111.230367 · PubMed

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…
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)

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