Crystal structure of arachidonic acid bound in the cyclooxygenase active site of pghs-1. Determined by X-ray diffraction at 3.0 Å resolution. Released 22 Sept 2000.
Explore 1DIY in 3D Show helices and sheets RCSB PDB PDBe
1DIY contains 37 α-helices and 34 β-strands across 1 chain. 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.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 35-37 | 3 | |
| α-helix | 45 | 1 | |
| β-strand | 46-50 | 5 | 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 | 99-104 | 6 | |
| α-helix | 108-121 | 14 | |
| 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 |
| β-strand | 161 | 1 | 7 |
| β-strand | 164 | 1 | 7 |
| α-helix | 174-181 | 8 | |
| 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 | 238-244 | 7 | |
| β-strand | 245 | 1 | 13 |
| β-strand | 252 | 1 | 13 |
| β-strand | 255-257 | 3 | 14 |
| β-strand | 260-262 | 3 | 14 |
| α-helix | 263-264 | 2 | |
| β-strand | 265 | 1 | 15 |
| 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 | 413-417 | 5 | |
| α-helix | 419-428 | 10 | |
| β-strand | 430 | 1 | 11 |
| β-strand | 432 | 1 | 9 |
| β-strand | 440 | 1 | 8 |
| α-helix | 445-458 | 14 | |
| α-helix | 460-462 | 3 | |
| α-helix | 463-469 | 7 | |
| α-helix | 473-475 | 3 | |
| α-helix | 478-481 | 4 | |
| α-helix | 486-495 | 10 | |
| α-helix | 498-500 | 3 | |
| α-helix | 503-509 | 7 | |
| α-helix | 511 | 1 | |
| β-strand | 512 | 1 | 17 |
| α-helix | 513 | 1 | |
| β-strand | 519 | 1 | 17 |
| α-helix | 520-535 | 16 | |
| α-helix | 538-540 | 3 | |
| α-helix | 547-549 | 3 | |
| α-helix | 553-560 | 8 | |
| α-helix | 564-569 | 6 | |
| β-strand | 581 | 1 | 10 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Prostaglandin H2 synthase-1 | A | protein | 553 | Ovis aries | P05979 (AlphaFold model) |
>1DIY_1 PROSTAGLANDIN H2 SYNTHASE-1 (chains A) PVNPCCYYPCQHQGICVRFGLDRYQCDCTRTGYSGPNCTIPEIWTWLRTTLRPSPSFIHF LLTHGRWLWDFVNATFIRDTLMRLVLTVRSNLIPSPPTYNIAHDYISWESFSNVSYYTRI LPSVPRDCPTPMGTKGKKQLPDAEFLSRRFLLRRKFIPDPQGTNLMFAFFAQHFTHQFFK TSGKMGPGFTKALGHGVDLGHIYGDNLERQYQLRLFKDGKLKYQMLNGEVYPPSVEEAPV LMHYPRGIPPQSQMAVGQEVFGLLPGLMLYATIWLREHNRVCDLLKAEHPTWGDEQLFQT ARLILIGETIKIVIEEYVQQLSGYFLQLKFDPELLFGAQFQYRNRIAMEFNQLYHWHPLM PDSFRVGPQDYSYEQFLFNTSMLVDYGVEALVDAFSRQPAGRIGGGRNIDHHILHVAVDV IKESRVLRLQPFNEYRKRFGMKPYTSFQELTGEKEMAAELEELYGDIDALEFYPGLLLEK CHPNSIFGESMIEMGAPFSLKGLLGNPICSPEYWKASTFGGEVGFNLVKTATLKKLVCLN TKTCPYVSFHVPD
| ID | Name | Formula | Copies |
|---|---|---|---|
| BOG | octyl beta-D-glucopyranoside | C14 H28 O6 | 4 |
| COH | Protoporphyrin IX containing co | C34 H32 Co N4 O4 | 1 |
| ACD | Arachidonic acid | C20 H32 O2 | 1 |
The productive conformation of arachidonic acid bound to prostaglandin synthase. Malkowski, M.G., Ginell, S.L., Smith, W.L. et al. Science (2000) 289:1933-1937. DOI 10.1126/science.289.5486.1933 · PubMed
Other PDB entries of the same protein (UniProt P05979 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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