2025-12-13_00000162|ligand|9NYD

Cryo-EM structure of the glycosyltransferase GtrB in the pre-catalysis and product-bound state; Electron microscopy 2.85Å
Protein #1 341 residues (91% resolved)

MHHHHHHSSGVDLGTENLYFQSNATIELSIVIPMYNEEDNLEHLFARLLEVLTPLKITYEIICVNDGSKDKTLKQLIDCYQSNRQIKIVNLSRNFGKEIALSAGIDYAQGNAVIPIDADLQDPPELIHELVDKWREGYDIVYATRRSRQGETWVKQFTAKMFYKVIGRMTEIKIPPNTGDFRLMDRKVVNAIKQLPERTRFMKGLFAWVGYRQTFVLFDREPRFQGQTKWNYWKLWNFALDGIFSFSLLPLKVWTYLGSIISLLSLAYASFLILKTITLGVDVPGYASLMVAILFLGGVQLISLGVIGEYLGRVYEEVKARPLYLVSDLWGLEYLPLEKLN

MHHHHHHSSGVDLGTENLYFQSNATIELSIVIPMYNEEDNLEHLFARLLEVLTPLKITYEIICVNDGSKDKTLKQLIDCYQSNRQIKIVNLSRNFGKEIALSAGIDYAQGNAVIPIDADLQDPPELIHELVDKWREGYDIVYATRRSRQGETWVKQFTAKMFYKVIGRMTEIKIPPNTGDFRLMDRKVVNAIKQLPERTRFMKGLFAWVGYRQTFVLFDREPRFQGQTKWNYWKLWNFALDGIFSFSLLPLKVWTYLGSIISLLSLAYASFLILKTITLGVDVPGYASLMVAILFLGGVQLISLGVIGEYLGRVYEEVKARPLYLVSDLWGLEYLPLEKLN
Non polymer #2 5TR

InChI=1S/C55H91O4P/c1-45(2)23-13-24-46(3)25-14-26-47(4)27-15-28-48(5)29-16-30-49(6)31-17-32-50(7)33-18-34-51(8)35-19-36-52(9)37-20-38-53(10)39-21-40-54(11)41-22-42-55(12)43-44-59-60(56,57)58/h23,25,27,29,31,33,35,37,39,41,43H,13-22,24,26,28,30,32,34,36,38,40,42,44H2,1-12H3,(H2,56,57,58)/b46-25+,47-27+,48-29+,49-31-,50-33+,51-35-,52-37+,53-39+,54-41+,55-43+

CC(=CCC/C(=C/CC/C(=C/CC/C(=C/CC/C(=C\CC/C(=C/CC/C(=C\CC/C(=C/CC/C(=C/CC/C(=C/CC/C(=C/COP(=O)(O)O)/C)/C)/C)/C)/C)/C)/C)/C)/C)/C)C
Non polymer #3 A1B94

InChI=1S/C61H101O9P/c1-46(2)23-13-24-47(3)25-14-26-48(4)27-15-28-49(5)29-16-30-50(6)31-17-32-51(7)33-18-34-52(8)35-19-36-53(9)37-20-38-54(10)39-21-40-55(11)41-22-42-56(12)43-44-68-71(66,67)70-61-60(65)59(64)58(63)57(45-62)69-61/h23,25,27,29,31,33,35,37,39,41,43,57-65H,13-22,24,26,28,30,32,34,36,38,40,42,44-45H2,1-12H3,(H,66,67)/b47-25?,48-27?,49-29?,50-31?,51-33?,52-35?,53-37?,54-39?,55-41+,56-43-/t57-,58+,59+,60-,61-/m0/s1

CC(=CCCC(=CCCC(=CCCC(=CCCC(=CCCC(=CCCC(=CCCC(=CCCC(=CCC/C(=C/CC/C(=C\COP(=O)(O)O[C@H]1[C@H]([C@@H]([C@@H]([C@@H](O1)CO)O)O)O)/C)/C)C)C)C)C)C)C)C)C)C
Non polymer #4 MG

InChI=1S/Mg/q+2

[Mg+2]
Non polymer #5 UDP

InChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1

C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
Non polymer #6 UPG

InChI=1S/C15H24N2O17P2/c18-3-5-8(20)10(22)12(24)14(32-5)33-36(28,29)34-35(26,27)30-4-6-9(21)11(23)13(31-6)17-2-1-7(19)16-15(17)25/h1-2,5-6,8-14,18,20-24H,3-4H2,(H,26,27)(H,28,29)(H,16,19,25)/t5-,6-,8-,9-,10+,11-,12-,13-,14-/m1/s1

C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)O)O
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Reference