Structure of PDB 2yy8 Chain A Binding Site BS01

Receptor Information
>2yy8 Chain A (length=174) Species: 53953 (Pyrococcus horikoshii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIVVLRLGHRPEDKRVTTHVALTARAFGADGIIIASEEDEKVKESVEDVV
KRWGGPFFIEFNRNWRKVMKEFTGVKVHLTMYGLHVDDVIEELKEKLKKG
EDFMIIVGAEKVPREVYELADYNVAIGNQPHSEVAALAVLLDRLLEGKGL
KKEFKGAKIKIVPQARGKKVVEVQ
Ligand information
Ligand IDMTA
InChIInChI=1S/C11H15N5O3S/c1-20-2-5-7(17)8(18)11(19-5)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17-18H,2H2,1H3,(H2,12,13,14)/t5-,7-,8-,11-/m1/s1
InChIKeyWUUGFSXJNOTRMR-IOSLPCCCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CSCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.341CSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 10.04n2c1c(ncnc1n(c2)C3OC(C(O)C3O)CSC)N
CACTVS 3.341CSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0CSC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
FormulaC11 H15 N5 O3 S
Name5'-DEOXY-5'-METHYLTHIOADENOSINE
ChEMBLCHEMBL277041
DrugBankDB02282
ZINCZINC000004228245
PDB chain2yy8 Chain A Residue 400 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2yy8 Crystal structure and mutational study of a unique SpoU family archaeal methylase that forms 2'-O-methylcytidine at position 56 of tRNA
Resolution2.48 Å
Binding residue
(original residue number in PDB)		L80 T81 M82 V108 G109 A110 E111 I127 H132 E134 A137
Binding residue
(residue number reindexed from 1)		L79 T80 M81 V107 G108 A109 E110 I126 H131 E133 A136
Annotation score3
Enzymatic activity
Enzyme Commision number 2.1.1.206: tRNA (cytidine(56)-2'-O)-methyltransferase.
Gene Ontology
Molecular Function
GO:0008168 methyltransferase activity
GO:0008175 tRNA methyltransferase activity
GO:0106059 tRNA (cytidine(56)-2'-O)-methyltransferase activity
Biological Process
GO:0002128 tRNA nucleoside ribose methylation
GO:0008033 tRNA processing
GO:0032259 methylation
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2yy8, PDBe:2yy8, PDBj:2yy8
PDBsum2yy8
PubMed18068186
UniProtO58214|TRM56_PYRHO tRNA (cytidine(56)-2'-O)-methyltransferase (Gene Name=PH0461)

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