Structure of PDB 6yjv Chain AAA Binding Site BS02

Receptor Information
>6yjv Chain AAA (length=504) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLAEIRTDFNILYSMMKKHEEFRWMRLRIRRMADAWIQAIKSLAEKQNLE
KRKRKKVLVHLGLLTKESGFKIAETAFSGGPLGELVQWSDLITSLYLLGH
DIRISASLAELKEIMGGGGVELIYIDIVGLAQFKKTLGPSWVHYQCMLRV
LDSFGTEPEFNHANYAQSKGHKTPWGKWNLNPQQFYTMFPHTPDNSFLGF
VVEQHLNINEIKRQNQSLVYGKVDSFWKNKKIYLDIIHTYMEVHATVYTK
NIPSYVKNHGILSGRDLQFLLRETKLFVGLGFPYEGPAPLEAIANGCAFL
NPKFNPPKSSKNTDFFIGKPTLRELTSQHPYAEVFIGRPHVWTVDLNNQE
EVEDAVKAILNQKIEPYMPYEFTCEGMLQRINAFIEKQDFCHVMWPPLSA
LQVKLAEPGQSCKQVCQESQLICEPSFFQHLNKDKDMLKYKVTCQSSELA
KDILVPSFDPKNKHCVFQGDLLLFSCAGAHPRHQRVCPCRDFIKGQVALC
KDCL
Ligand information
Ligand IDU2F
InChIInChI=1S/C15H23FN2O16P2/c16-8-11(23)9(21)5(3-19)32-14(8)33-36(28,29)34-35(26,27)30-4-6-10(22)12(24)13(31-6)18-2-1-7(20)17-15(18)25/h1-2,5-6,8-14,19,21-24H,3-4H2,(H,26,27)(H,28,29)(H,17,20,25)/t5-,6-,8-,9-,10-,11-,12-,13-,14-/m1/s1
InChIKeyNGTCPFGWXMBZEP-NQQHDEILSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(OC1OC(C(O)C(O)C1F)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)CO)O)O)F)O)O
CACTVS 3.341OC[C@H]1O[C@H](O[P@](O)(=O)O[P@@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@H](F)[C@@H](O)[C@@H]1O
OpenEye OEToolkits 1.5.0C1=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)F)O)O
CACTVS 3.341OC[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](F)[CH](O)[CH]1O
FormulaC15 H23 F N2 O16 P2
NameURIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE
ChEMBLCHEMBL593830
DrugBankDB03488
ZINCZINC000016051573
PDB chain6yjv Chain AAA Residue 806 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6yjv Substrate Engagement and Catalytic Mechanisms of N-Acetylglucosaminyltransferase V
Resolution1.7 Å
Binding residue
(original residue number in PDB)		G292 G293 P294 L295 G296 Y439 K441 P505 G508 P509 A510 E513
Binding residue
(residue number reindexed from 1)		G79 G80 P81 L82 G83 Y220 K222 P283 G286 P287 A288 E291
Annotation score3
Enzymatic activity
Enzyme Commision number 2.4.1.155: alpha-1,6-mannosyl-glycoprotein 6-beta-N-acetylglucosaminyltransferase.
Gene Ontology
Molecular Function
GO:0030144 alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity
Biological Process
GO:0006487 protein N-linked glycosylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6yjv, PDBe:6yjv, PDBj:6yjv
PDBsum6yjv
PubMed
UniProtQ09328|MGT5A_HUMAN Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase A (Gene Name=MGAT5)

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