Structure of PDB 2yy8 Chain B Binding Site BS01

Receptor Information
>2yy8 Chain B (length=174) Species: 53953 (Pyrococcus horikoshii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIVVLRLGHRPERDKRVTTHVALTARAFGADGIIIASEEDEKVKESVEDV
VKRWGGPFFIEFNRNWRKVMKEFTGVKVHLTMYGLHVDDVIEELKEKLKK
GEDFMIIVGAEKVPREVYELADYNVAIGNQPHSEVAALAVLLDRLLEGKG
LKKEFKGAKIKIVPQARGKKVVEV
Ligand information
Ligand IDSAM
InChIInChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
InChIKeyMEFKEPWMEQBLKI-FCKMPRQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[S@@+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.341C[S+](CC[CH](N)C([O-])=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[S@@+](CC[C@@H](C(=O)[O-])N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
ACDLabs 10.04[O-]C(=O)C(N)CC[S+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H22 N6 O5 S
NameS-ADENOSYLMETHIONINE
ChEMBLCHEMBL1235831
DrugBank
ZINC
PDB chain2yy8 Chain B Residue 500 [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 K112 V113 I127 G128 H132 E134 A137
Binding residue
(residue number reindexed from 1)		L80 T81 M82 V108 G109 A110 K112 V113 I127 G128 H132 E134 A137
Annotation score5
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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