Structure of PDB 6fdf Chain A Binding Site BS01

Receptor Information
>6fdf Chain A (length=325) Species: 4896 (Schizosaccharomyces pombe) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RLRVLELYSGIGGMHYALNLANIPADIVCAIDINPQANEIYNLNHGKLAK
HMDISTLTAKDFDAFDCKLWTMSPSCQPFTRIGNRKDILDPRSQAFLNIL
NVLPHVNNLPEYILIENVQGFEESKAAEECRKVLRNCGYNLIEGILSPNQ
FNIPNSRSRWYGLARLNFKGEWSIDDVFQFSEVAQKEGEVKRIRDYLEIE
RDWSSYMVLESVLNKWGHQFDIVKPDSSSCCCFTRGYTHLVQGAGSILQM
SDHENTHEQFERNRMALQLRYFTAREVARLMGFPESLEWSKSNVTEKCMY
RLLGNSINVKVVSYLISLLLEPLNF
Ligand information
Ligand IDSAH
InChIInChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
InChIKeyZJUKTBDSGOFHSH-WFMPWKQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
CACTVS 3.341N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
ACDLabs 10.04O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N
FormulaC14 H20 N6 O5 S
NameS-ADENOSYL-L-HOMOCYSTEINE
ChEMBLCHEMBL418052
DrugBankDB01752
ZINCZINC000004228232
PDB chain6fdf Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6fdf Structural insights into the stimulation of S. pombe Dnmt2 catalytic efficiency by the tRNA nucleoside queuosine.
Resolution1.697 Å
Binding residue
(original residue number in PDB)		Y13 S14 G15 I16 G18 D37 I38 M57 D58 I59 S78 N310 I312
Binding residue
(residue number reindexed from 1)		Y8 S9 G10 I11 G13 D32 I33 M52 D53 I54 S73 N305 I307
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) C81 E121 R162 R164
Catalytic site (residue number reindexed from 1) C76 E116 R157 R159
Enzyme Commision number 2.1.1.204: tRNA (cytosine(38)-C(5))-methyltransferase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0003723 RNA binding
GO:0008168 methyltransferase activity
GO:0009008 DNA-methyltransferase activity
GO:0016427 tRNA (cytidine) methyltransferase activity
GO:0016428 tRNA (cytidine-5-)-methyltransferase activity
Biological Process
GO:0002946 tRNA C5-cytosine methylation
GO:0008033 tRNA processing
GO:0032259 methylation
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6fdf, PDBe:6fdf, PDBj:6fdf
PDBsum6fdf
PubMed29892076
UniProtP40999|PMT1M_SCHPO tRNA (cytosine(38)-C(5))-methyltransferase (Gene Name=pmt1)

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