6OFY: Arachidonic Acid

Crystal Structure of Arachidonic Acid bound to V349I murine COX-2. Determined by X-ray diffraction at 2.2 Å resolution. Released 5 Feb 2020.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Mus musculus
Chains: 2
Atoms: 9,754
Mol. weight: 131.21 kDa
Ligands: ACD, AKR, BOG, COH
Released: 5 Feb 2020

Explore 6OFY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6OFY contains 91 α-helices and 64 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: 46 helices, 32 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	73	1
α-helix	74-82	9
α-helix	83-85	3
α-helix	86-93	8
α-helix	97-103	7
α-helix	107-120	14
β-strand	131	1	3
β-strand	132	1	4
β-strand	135	1	4
α-helix	140-144	5
β-strand	148	1	5
α-helix	149	1
β-strand	150	1	6
β-strand	151	1	3
α-helix	154-157	4
β-strand	162	1	7
β-strand	165	1	7
α-helix	172-174	3
α-helix	175-178	4
α-helix	179-183	5
β-strand	184	1	8
β-strand	190	1	9
β-strand	195	1	10
β-strand	196	1	11
α-helix	197-207	11
β-strand	213	1	12
β-strand	221	1	5
β-strand	222	1	12
α-helix	232-235	4
α-helix	239-245	7
β-strand	246	1	13
α-helix	252	1
β-strand	253	1	13
α-helix	254	1
β-strand	256-258	3	14
β-strand	261-263	3	14
β-strand	266	1	15
α-helix	267-270	4
α-helix	282-284	3
β-strand	286	1	15
α-helix	293-295	3
α-helix	297-320	24
α-helix	326-344	19
α-helix	345-350	6
α-helix	351-354	4
α-helix	364-367	4
β-strand	379	1	6
α-helix	380-385	6
α-helix	389-391	3
β-strand	396-398	3	16
β-strand	401-403	3	16
α-helix	405-408	4
α-helix	413-418	6
α-helix	420-429	10
β-strand	431	1	11
α-helix	432	1
β-strand	433	1	9
α-helix	434	1
β-strand	441	1	8
α-helix	443-445	3
α-helix	446-458	13
α-helix	464-470	7
α-helix	474-476	3
α-helix	479-483	5
α-helix	487-496	10
α-helix	499-501	3
α-helix	504-510	7
α-helix	512-513	2
α-helix	521-536	16
α-helix	539-541	3
α-helix	548-551	4
α-helix	554-561	8
α-helix	565-572	8
β-strand	582	1	10

Chain B: 45 helices, 32 β-strands

Element	Residues	Length	Sheet
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	97-103	7
α-helix	107-120	14
β-strand	131-132	2	19
β-strand	135	1	19
α-helix	140-144	5
β-strand	148	1	20
α-helix	149	1
β-strand	150-151	2	19
α-helix	154-157	4
β-strand	162	1	21
β-strand	165	1	21
α-helix	172-174	3
α-helix	175-178	4
α-helix	179-183	5
β-strand	184	1	22
β-strand	190	1	23
β-strand	195	1	24
β-strand	196	1	25
α-helix	197-207	11
β-strand	213	1	26
β-strand	221	1	20
β-strand	222	1	26
α-helix	232-235	4
α-helix	239-245	7
β-strand	246	1	27
α-helix	252	1
β-strand	253	1	27
α-helix	254	1
β-strand	256-258	3	28
β-strand	261-263	3	28
β-strand	266	1	29
α-helix	267-270	4
α-helix	282-284	3
β-strand	286	1	29
α-helix	293-295	3
α-helix	297-320	24
α-helix	326-344	19
α-helix	345-350	6
α-helix	351-354	4
α-helix	364-367	4
β-strand	379	1	19
α-helix	380-385	6
α-helix	389-391	3
β-strand	396-398	3	30
β-strand	401-403	3	30
α-helix	405-408	4
α-helix	413-418	6
α-helix	420-429	10
β-strand	431	1	25
α-helix	432	1
β-strand	433	1	23
α-helix	434	1
β-strand	441	1	22
α-helix	443-445	3
α-helix	446-458	13
α-helix	464-470	7
α-helix	474-476	3
α-helix	479-483	5
α-helix	487-496	10
α-helix	499-501	3
α-helix	504-510	7
α-helix	512	1
β-strand	513	1	31
β-strand	520	1	31
α-helix	521-536	16
α-helix	539-541	3
α-helix	548-551	4
α-helix	554-561	8
α-helix	565-572	8
β-strand	582	1	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Prostaglandin G/H synthase 2	A, B	protein	552	Mus musculus	Q05769 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6OFY_1 Prostaglandin G/H synthase 2 (chains A, B)
HHHPCCSNPCQNRGECMSTGFDQYKCDCTRTGFYGENCTTPEFLTRIKLLLKPTPNTVHY
ILTHFKGVWNIVNNIPFLRSLIMKYVLTSRSYLIDSPPTYNVHYGYKSWEAFSNLSYYTR
ALPPVADDCPTPMGVKGNKELPDSKEVLEKVLLRREFIPDPQGSNMMFAFFAQHFTHQFF
KTDHKRGPGFTRGLGHGVDLNHIYGETLDRQHKLRLFKDGKLKYQVIGGEVYPPTVKDTQ
VEMIYPPHIPENLQFAVGQEVFGLVPGLMMYATIWLREHNRVCDILKQEHPEWGDEQLFQ
TSRLILIGETIKIVIEDYIQHLSGYHFKLKFDPELLFNQQFQYQNRIASEFNTLYHWHPL
LPDTFNIEDQEYSFKQFLYNNSILLEHGLTQFVESFTRQIAGRVAGGRNVPIAVQAVAKA
SIDQSREMKYQSLNEYRKRFSLKPYTSFEELTGEKEMAAELKALYSDIDVMELYPALLVE
KPRPDAIFGETMVELGAPFSLKGLMGNPICSPQYWKPSTFGGEVGFKIINTASIQSLICN
NVKGCPFTSFNV

Ligands and cofactors

ID	Name	Formula	Copies
ACD	Arachidonic acid	C20 H32 O2	2
AKR	Acrylic acid	C3 H4 O2	1
BOG	octyl beta-D-glucopyranoside	C14 H28 O6	1
COH	Protoporphyrin IX containing co	C34 H32 Co N4 O4	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8

Primary citation

Arg-513 and Leu-531 Are Key Residues Governing Time-Dependent Inhibition of Cyclooxygenase-2 by Aspirin and Celebrex. Dong, L., Anderson, A.J., Malkowski, M.G. Biochemistry (2019) 58:3990-4002. DOI 10.1021/acs.biochem.9b00659 · 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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