2026-01-10_00000468|ligand|9VVO

cryo-EM structure of gastric proton pump bound to YK01; Electron microscopy 2.66Å
Protein #1 983 residues (100% resolved)

NDHQLSVAELEQKYQTSATKGLSASLAAELLLRDGPNALRPPRGTPEYVKFARQLAGGLQCLMWVAAAICLIAFAIQASEGDLTTDDNLYLALALIAVVVVTGCFGYYQEFKSTNIIASFKNLVPQQATVIRDGDKFQINADQLVVGDLVEMKGGDRVPADIRILQAQGCKVDNSSLTGESEPQTRSPECTHESPLETRNIAFFSTMCLEGTAQGLVVNTGDRTIIGRIASLASGVENEKTPIAIEIEHFVDIIAGLAILFGATFFIVAMCIGYTFLRAMVFFMAIVVAYVPEGLLATVTVCLSLTAKRLASKNCVVKNLEAVETLGSTSVICS(BFD)KTGTLTQNRMTVSHLWFDNHIHSADTTEDQSGQTFDQSSETWRALCRVLTLCNRAAFKSGQDAVPVPKRIVIGDASETALLKFSELTLGNAMGYRERFPKVCEIPFNSTNKFQLSIHTLEDPRDPRHVLVMKGAPERVLERCSSILIKGQELPLDEQWREAFQTAYLSLGGLGERVLGFCQLYLSEKDYPPGYAFDVEAMNFPTSGLCFAGLVSMIDPPRATVPDAVLKCRTAGIRVIMVTGDHPITAKAIAASVGIISEGSETVEDIAARLRVPVDQVNRKDARACVINGMQLKDMDPSELVEALRTHPEMVFARTSPQQKLVIVESCQRLGAIVAVTGDGVNDSPALKKADIGVAMGIAGSDAAKNAADMILLDDNFASIVTGVEQGRLIFDNLKKSIAYTLTKNIPELTPYLIYITVSVPLPLGCITILFIELCTDIFPSVSLAYEKAESDIMHLRPRNPKRDRLVNEPLAAYSYFQIGAIQSFAGFTDYFTAMAQEGWFPLLCVGLRPQWENHHLQDLQDSYGQEWTFGQRLYQQYTCYTVFFISIEMCQIADVLIRKTRRLSAFQQGFFRNRILVIAIVFQVCIGCFLCYCPGMPNIFNFMPIRFQWWLVPMPFSLLIFVYDEIRKLGVRCCPGSWWDQELYY

NDHQLSVAELEQKYQTSATKGLSASLAAELLLRDGPNALRPPRGTPEYVKFARQLAGGLQCLMWVAAAICLIAFAIQASEGDLTTDDNLYLALALIAVVVVTGCFGYYQEFKSTNIIASFKNLVPQQATVIRDGDKFQINADQLVVGDLVEMKGGDRVPADIRILQAQGCKVDNSSLTGESEPQTRSPECTHESPLETRNIAFFSTMCLEGTAQGLVVNTGDRTIIGRIASLASGVENEKTPIAIEIEHFVDIIAGLAILFGATFFIVAMCIGYTFLRAMVFFMAIVVAYVPEGLLATVTVCLSLTAKRLASKNCVVKNLEAVETLGSTSVICSDKTGTLTQNRMTVSHLWFDNHIHSADTTEDQSGQTFDQSSETWRALCRVLTLCNRAAFKSGQDAVPVPKRIVIGDASETALLKFSELTLGNAMGYRERFPKVCEIPFNSTNKFQLSIHTLEDPRDPRHVLVMKGAPERVLERCSSILIKGQELPLDEQWREAFQTAYLSLGGLGERVLGFCQLYLSEKDYPPGYAFDVEAMNFPTSGLCFAGLVSMIDPPRATVPDAVLKCRTAGIRVIMVTGDHPITAKAIAASVGIISEGSETVEDIAARLRVPVDQVNRKDARACVINGMQLKDMDPSELVEALRTHPEMVFARTSPQQKLVIVESCQRLGAIVAVTGDGVNDSPALKKADIGVAMGIAGSDAAKNAADMILLDDNFASIVTGVEQGRLIFDNLKKSIAYTLTKNIPELTPYLIYITVSVPLPLGCITILFIELCTDIFPSVSLAYEKAESDIMHLRPRNPKRDRLVNEPLAAYSYFQIGAIQSFAGFTDYFTAMAQEGWFPLLCVGLRPQWENHHLQDLQDSYGQEWTFGQRLYQQYTCYTVFFISIEMCQIADVLIRKTRRLSAFQQGFFRNRILVIAIVFQVCIGCFLCYCPGMPNIFNFMPIRFQWWLVPMPFSLLIFVYDEIRKLGVRCCPGSWWDQELYY
Protein #2 268 residues (100% resolved)

NPDTGQMLGRTLSRWVWISLYYVAFYVVMSGIFALCIYVLMRTIDPYTPDYQDQLKSPGVTLRPDVYGEKGLDISYNVSDSTTWAGLAHTLHRFLAGYSPAAQEGSINCTSEKYFFQESFLAPNHTKFSCKFTADMLQNCSGRPDPTFGFAEGKPCFIIKMNRIVKFLPGNSTAPRVDCAFLDQPRDGPPLQVEYFPANGTYSLHYFPYYGKKAQPHYSNPLVAAKLLNVPRNRDVVIVCKILAEHVSFDNPHDPYEGKVEFKLKIQK

NPDTGQMLGRTLSRWVWISLYYVAFYVVMSGIFALCIYVLMRTIDPYTPDYQDQLKSPGVTLRPDVYGEKGLDISYNVSDSTTWAGLAHTLHRFLAGYSPAAQEGSINCTSEKYFFQESFLAPNHTKFSCKFTADMLQNCSGRPDPTFGFAEGKPCFIIKMNRIVKFLPGNSTAPRVDCAFLDQPRDGPPLQVEYFPANGTYSLHYFPYYGKKAQPHYSNPLVAAKLLNVPRNRDVVIVCKILAEHVSFDNPHDPYEGKVEFKLKIQK
Non polymer #3 A1MA7

InChI=1S/C23H29N3/c1-24-11-17-7-9-19(10-8-17)13-26-15-21-20-14-25(16-22(26)23(20)21)12-18-5-3-2-4-6-18/h2-10,20-24H,11-16H2,1H3/t20-,21+,22-,23-/m1/s1

CNCc1ccc(cc1)CN2C[C@H]3[C@@H]4[C@H]3[C@H]2CN(C4)Cc5ccccc5
Non polymer #4 CLR

InChI=1S/C27H46O/c1-18(2)7-6-8-19(3)23-11-12-24-22-10-9-20-17-21(28)13-15-26(20,4)25(22)14-16-27(23,24)5/h9,18-19,21-25,28H,6-8,10-17H2,1-5H3/t19-,21+,22+,23-,24+,25+,26+,27-/m1/s1

CC(C)CCC[C@@H](C)[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3[C@H]2CC=C4[C@@]3(CC[C@@H](C4)O)C)C
Non polymer #5 MG

InChI=1S/Mg/q+2

[Mg+2]
Non polymer #6 NAG

InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1

CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@H]1O)CO)O)O
Non polymer #7 PCW

InChI=1S/C44H84NO8P/c1-6-8-10-12-14-16-18-20-22-24-26-28-30-32-34-36-43(46)50-40-42(41-52-54(48,49)51-39-38-45(3,4)5)53-44(47)37-35-33-31-29-27-25-23-21-19-17-15-13-11-9-7-2/h20-23,42H,6-19,24-41H2,1-5H3/p+1/b22-20-,23-21-/t42-/m1/s1

CCCCCCCC\C=C/CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OCC[N+](C)(C)C)OC(=O)CCCCCCC\C=C/CCCCCCCC
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Reference